##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=FAIL,Description="Fail the site if all alleles fail but for different reasons.">
##FILTER=<ID=base_qual,Description="alt median base quality">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=possible_numt,Description="Allele depth is below expected coverage of NuMT in autosome">
##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=FAD,Number=R,Type=Integer,Description="Count of fragments supporting each allele.">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output results/variant_calls/pakistan1_filtered.vcf.gz --stats results/variant_calls/raw/pakistan1_unfiltered.vcf.gz.stats --orientation-bias-artifact-priors results/variant_calls/raw/read_orientation_model/pakistan1_read-orientation-model.tar.gz --variant results/variant_calls/raw/pakistan1_unfiltered.vcf.gz --reference resources/hg38.fa --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --microbial-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality -1 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false",Version="4.2.5.0",Date="March 22, 2022 at 11:15:16 AM UTC">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --f1r2-tar-gz results/variant_calls/read_orientation_model/f1r2_files/pakistan1_chr8_f1r2.tar.gz --panel-of-normals /rds/project/rds-uBnw8vu2KfY/new_brno_wes/resources/1000g_pon.hg38.vcf.gz --germline-resource /rds/project/rds-uBnw8vu2KfY/new_brno_wes/resources/af-only-gnomad.hg38.vcf.gz --output results/variant_calls/raw/pakistan1_chr8_unfiltered.vcf.gz --intervals chr8 --input results/mapped/pakistan1_PS-9941-44_tumour.bam --reference resources/hg38.fa --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --training-data-mode false --training-data-mode-ref-downsample 2147483647 --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --pruning-seeding-lod-threshold 9.210340371976184 --max-unpruned-variants 100 --linked-de-bruijn-graph false --disable-artificial-haplotype-recovery false --enable-legacy-graph-cycle-detection false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --num-matching-bases-in-dangling-end-to-recover -1 --error-correction-log-odds -Infinity --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --base-quality-score-threshold 18 --dragstr-het-hom-ratio 2 --dont-use-dragstr-pair-hmm-scores false --pair-hmm-gap-continuation-penalty 10 --expected-mismatch-rate-for-read-disqualification 0.02 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --disable-symmetric-hmm-normalizing false --disable-cap-base-qualities-to-map-quality false --enable-dynamic-read-disqualification-for-genotyping false --dynamic-read-disqualification-threshold 1.0 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipped-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --max-mnp-distance 1 --force-call-filtered-alleles false --soft-clip-low-quality-ends false --allele-informative-reads-overlap-margin 2 --smith-waterman-dangling-end-match-value 25 --smith-waterman-dangling-end-mismatch-penalty -50 --smith-waterman-dangling-end-gap-open-penalty -110 --smith-waterman-dangling-end-gap-extend-penalty -6 --smith-waterman-haplotype-to-reference-match-value 200 --smith-waterman-haplotype-to-reference-mismatch-penalty -150 --smith-waterman-haplotype-to-reference-gap-open-penalty -260 --smith-waterman-haplotype-to-reference-gap-extend-penalty -11 --smith-waterman-read-to-haplotype-match-value 10 --smith-waterman-read-to-haplotype-mismatch-penalty -15 --smith-waterman-read-to-haplotype-gap-open-penalty -30 --smith-waterman-read-to-haplotype-gap-extend-penalty -5 --min-assembly-region-size 50 --max-assembly-region-size 300 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --assembly-region-padding 100 --padding-around-indels 75 --padding-around-snps 20 --padding-around-strs 75 --max-extension-into-assembly-region-padding-legacy 25 --max-reads-per-alignment-start 50 --enable-legacy-assembly-region-trimming false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --max-variants-per-shard 0 --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays  --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.2.5.0",Date="March 17, 2022 at 7:35:17 AM UTC">
##INFO=<ID=AS_FilterStatus,Number=A,Type=String,Description="Filter status for each allele, as assessed by ApplyVQSR. Note that the VCF filter field will reflect the most lenient/sensitive status across all alleles.">
##INFO=<ID=AS_SB_TABLE,Number=1,Type=String,Description="Allele-specific forward/reverse read counts for strand bias tests. Includes the reference and alleles separated by |.">
##INFO=<ID=AS_UNIQ_ALT_READ_COUNT,Number=A,Type=Integer,Description="Number of reads with unique start and mate end positions for each alt at a variant site">
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality by allele">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length by allele">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality by allele">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##INFO=<ID=RPA,Number=R,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
##MutectVersion=2.2
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
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##contig=<ID=chrUn_KI270372v1,length=1650>
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##contig=<ID=chrUn_KI270375v1,length=2378>
##contig=<ID=chrUn_KI270371v1,length=2805>
##contig=<ID=chrUn_KI270448v1,length=7992>
##contig=<ID=chrUn_KI270521v1,length=7642>
##contig=<ID=chrUn_GL000195v1,length=182896>
##contig=<ID=chrUn_GL000219v1,length=179198>
##contig=<ID=chrUn_GL000220v1,length=161802>
##contig=<ID=chrUn_GL000224v1,length=179693>
##contig=<ID=chrUn_KI270741v1,length=157432>
##contig=<ID=chrUn_GL000226v1,length=15008>
##contig=<ID=chrUn_GL000213v1,length=164239>
##contig=<ID=chrUn_KI270743v1,length=210658>
##contig=<ID=chrUn_KI270744v1,length=168472>
##contig=<ID=chrUn_KI270745v1,length=41891>
##contig=<ID=chrUn_KI270746v1,length=66486>
##contig=<ID=chrUn_KI270747v1,length=198735>
##contig=<ID=chrUn_KI270748v1,length=93321>
##contig=<ID=chrUn_KI270749v1,length=158759>
##contig=<ID=chrUn_KI270750v1,length=148850>
##contig=<ID=chrUn_KI270751v1,length=150742>
##contig=<ID=chrUn_KI270752v1,length=27745>
##contig=<ID=chrUn_KI270753v1,length=62944>
##contig=<ID=chrUn_KI270754v1,length=40191>
##contig=<ID=chrUn_KI270755v1,length=36723>
##contig=<ID=chrUn_KI270756v1,length=79590>
##contig=<ID=chrUn_KI270757v1,length=71251>
##contig=<ID=chrUn_GL000214v1,length=137718>
##contig=<ID=chrUn_KI270742v1,length=186739>
##contig=<ID=chrUn_GL000216v2,length=176608>
##contig=<ID=chrUn_GL000218v1,length=161147>
##contig=<ID=chrEBV,length=171823>
##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
##source=FilterMutectCalls
##source=Mutect2
##tumor_sample=pakistan1_PS-9941-44_tumour
##bcftools_normVersion=1.14+htslib-1.14
##bcftools_normCommand=norm -c w -m- -f resources/hg38.fa -Oz -o results/variants_calls/pakistan1_normalised.vcf.gz results/variant_calls/pakistan1_filtered.vcf.gz; Date=Wed Mar 23 15:01:59 2022
##VEP="v105" time="2022-03-23 15:02:31" cache="resources/ensembl-vep-data/homo_sapiens/105_GRCh38" db="homo_sapiens_core_105_38@ensembldb.ensembl.org" ensembl-variation=105.ac8178e ensembl-funcgen=105.660df8f ensembl-io=105.2a0a40c ensembl=105.525fbcb 1000genomes="phase3" COSMIC="92" ClinVar="202106" ESP="V2-SSA137" HGMD-PUBLIC="20204" assembly="GRCh38.p13" dbSNP="154" gencode="GENCODE 39" genebuild="2014-07" gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS">
##bcftools_filterVersion=1.14+htslib-1.14
##bcftools_filterCommand=filter -i FILTER="PASS" -Ov results/vep/pakistan1.vcf.gz; Date=Thu Mar 31 17:26:24 2022
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	pakistan1_PS-9941-44_tumour
chr1	13421	.	A	AAATGTGATCTCTCTCGGGG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=3,9|0,3;DP=17;ECNT=2;GERMQ=7;MBQ=29,20;MFRL=174,107;MMQ=34,44;MPOS=20;POPAF=7.3;ROQ=93;TLOD=9.87;CSQ=AATGTGATCTCTCTCGGGG|intron_variant&non_coding_transcript_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene||5/5|ENST00000450305.2:n.415-32_415-31insAATGTGATCTCTCTCGGGG|||||||||1||insertion|HGNC|HGNC:37102|YES||||||||||||||||||||||||||||||||||||||||||||,AATGTGATCTCTCTCGGGG|non_coding_transcript_exon_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|3/3||ENST00000456328.2:n.669_670insAATGTGATCTCTCTCGGGG||669-670|||||||1||insertion|HGNC|HGNC:37102||||1|||||||||||||||||||||||||||||||||||||||||,AATGTGATCTCTCTCGGGG|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||982|-1||insertion|HGNC|HGNC:38034|YES||||||||||||||||||||||||||||||||||||||||||||,AATGTGATCTCTCTCGGGG|downstream_gene_variant|MODIFIER|MIR6859-1|ENSG00000278267|Transcript|ENST00000619216|miRNA|||||||||||3947|-1||insertion|HGNC|HGNC:50039|YES||||||||||||||||||||||||||||||||||||||||||||,AATGTGATCTCTCTCGGGG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344265|CTCF_binding_site||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||,AATGTGATCTCTCTCGGGG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164745|promoter_flanking_region||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:12,3:0.282:15:4,2:2,0:10,3:1|0:13417_C_CGAGA:13417:3,9,0,3
chr1	647483	.	A	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;GERMQ=32;MBQ=0,20;MFRL=0,82;MMQ=60,37;MPOS=13;POPAF=7.3;ROQ=33;TLOD=4.61;CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000419394|processed_transcript||3/3|ENST00000419394.2:n.480+56202T>G|||||||rs1276696238||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000440200|processed_transcript||1/2|ENST00000440200.5:n.170-39427T>G|||||||rs1276696238||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000634337|processed_transcript||2/4|ENST00000634337.2:n.161-39427T>G|||||||rs1276696238||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000635509|processed_transcript||2/3|ENST00000635509.2:n.313-45906T>G|||||||rs1276696238||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000648019|processed_transcript||5/7|ENST00000648019.1:n.636-39427T>G|||||||rs1276696238||-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,2:0.667:2:0,0:0,1:0,1:0,0,1,1
chr1	674844	.	A	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=35,9|3,2;DP=53;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=128,166;MMQ=50,60;MPOS=53;POPAF=7.3;ROQ=3;TLOD=8.26;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000419394|processed_transcript||3/3|ENST00000419394.2:n.480+28841T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|WBP1LP6|ENSG00000268663|Transcript|ENST00000438434|processed_pseudogene|1/1||ENST00000438434.2:n.3A>T||3|||||||1||SNV|HGNC|HGNC:43956|YES||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000440200|processed_transcript||1/2|ENST00000440200.5:n.169+45188T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000634337|processed_transcript||2/4|ENST00000634337.2:n.160+24083T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000635509|processed_transcript||2/3|ENST00000635509.2:n.312+36867T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000648019|processed_transcript||5/7|ENST00000648019.1:n.635+24083T>A|||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:44,5:0.099:49:21,0:13,3:35,3:35,9,3,2
chr1	778107	.	T	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,100;MMQ=60,39;MPOS=8;POPAF=7.3;ROQ=28;TLOD=3.88;CSQ=A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000412115|lncRNA|||||||||||640|1||SNV|HGNC|HGNC:50701|YES|||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000428504|transcribed_unprocessed_pseudogene|||||||||||3827|-1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000429505|lncRNA|||||||||||653|1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000434264|lncRNA|||||||||||663|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000443772|lncRNA|||||||||||865|1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000457084|lncRNA|||||||||||675|1||SNV|HGNC|HGNC:50701||||4|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000506640|processed_transcript||1/15|ENST00000506640.2:n.343+177A>T|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000589899|lncRNA|||||||||||823|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000609830|lncRNA|||||||||||830|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000634337|processed_transcript||1/4|ENST00000634337.2:n.127+49563A>T|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000635509|processed_transcript||1/3|ENST00000635509.2:n.100+49563A>T|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER||ENSG00000285268|Transcript|ENST00000644482|transcribed_processed_pseudogene|||||||||||3830|1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000651411|lncRNA|||||||||||742|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000655765|lncRNA|||||||||||640|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000656571|lncRNA|||||||||||695|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000657896|lncRNA|||||||||||653|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000658648|lncRNA|||||||||||689|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000665719|lncRNA|||||||||||705|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000665867|lncRNA|||||||||||702|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000666217|lncRNA|||||||||||705|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000669749|lncRNA|||||||||||702|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000670700|lncRNA|||||||||||651|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000685466|processed_transcript|||||||||||157|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000691293|processed_transcript|||||||||||157|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000692781|processed_transcript|||||||||||157|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000081|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00008420972|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0014|10|Y|-0.099|ATF4::CEBPB&ATF4::CEBPD&ATF4::TEF&ATF4&CEBPG::ATF4	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,0,1
chr1	781965	.	A	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=55,25|3,1;DP=86;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=115,154;MMQ=53,44;MPOS=27;POPAF=7.3;ROQ=2;TLOD=4.69;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000412115|lncRNA||1/4|ENST00000412115.2:n.346+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|YES|||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000429505|lncRNA||1/3|ENST00000429505.6:n.333+2873A>T|||||||||1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000434264|lncRNA|2/3||ENST00000434264.6:n.352A>T||352|||||||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000443772|lncRNA||1/3|ENST00000443772.2:n.121+2873A>T|||||||||1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000457084|lncRNA|2/2||ENST00000457084.1:n.340A>T||340|||||||1||SNV|HGNC|HGNC:50701||||4|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000506640|processed_transcript|||||||||||3339|-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000585745|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000585768|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000585826|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000586288|lncRNA|||||||||||2431|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000586928|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000587530|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000588951|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000589531|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000589899|lncRNA|2/4||ENST00000589899.5:n.192A>T||192|||||||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000590848|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000591440|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000591702|lncRNA|||||||||||3835|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000592547|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000593022|lncRNA|||||||||||2405|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000609830|lncRNA|2/4||ENST00000609830.1:n.185A>T||185|||||||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000634337|processed_transcript||1/4|ENST00000634337.2:n.127+45705T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000635509|processed_transcript||1/3|ENST00000635509.2:n.100+45705T>A|||||||||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER||ENSG00000285268|Transcript|ENST00000644482|transcribed_processed_pseudogene|1/1||ENST00000644482.1:n.29A>T||29|||||||1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000651411|lncRNA||1/3|ENST00000651411.1:n.244+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000655765|lncRNA||1/2|ENST00000655765.1:n.346+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000656571|lncRNA||1/4|ENST00000656571.1:n.291+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000657896|lncRNA||1/3|ENST00000657896.1:n.333+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000658648|lncRNA||1/4|ENST00000658648.1:n.297+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000665719|lncRNA||1/4|ENST00000665719.1:n.281+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000665867|lncRNA||1/1|ENST00000665867.1:n.284+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000666217|lncRNA||1/3|ENST00000666217.1:n.281+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000669749|lncRNA||1/3|ENST00000669749.1:n.284+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000670700|lncRNA||1/4|ENST00000670700.1:n.335+2873A>T|||||||||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000685466|processed_transcript|||||||||||3327|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000691293|processed_transcript|||||||||||3327|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000228327|Transcript|ENST00000692781|processed_transcript|||||||||||3296|-1||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:80,4:0.058:84:34,0:27,3:64,3:55,25,3,1
chr1	805966	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=4,4|1,1;DP=10;ECNT=1;GERMQ=11;MBQ=20,20;MFRL=157,160;MMQ=47,47;MPOS=31;POPAF=4.61;ROQ=3;TLOD=3.47;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000412115|lncRNA||3/4|ENST00000412115.2:n.809+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|YES|||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000429505|lncRNA||||||||||rs1383404615|696|1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000443772|lncRNA||3/3|ENST00000443772.2:n.613+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230092|Transcript|ENST00000447500|processed_transcript||3/4|ENST00000447500.4:n.495-75G>A|||||||rs1383404615||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000585768|lncRNA||||||||||rs1383404615|4090|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000586288|lncRNA||6/6|ENST00000586288.1:n.935+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000587530|lncRNA||||||||||rs1383404615|696|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000588951|lncRNA||2/3|ENST00000588951.5:n.429-1251C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000589531|lncRNA||3/3|ENST00000589531.5:n.616+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230092|Transcript|ENST00000590817|transcribed_unprocessed_pseudogene||2/2|ENST00000590817.3:n.146-75G>A|||||||rs1383404615||-1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000590848|lncRNA||||||||||rs1383404615|1134|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000591440|lncRNA||||||||||rs1383404615|839|1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000593022|lncRNA||3/3|ENST00000593022.5:n.620-420C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000634337|processed_transcript||1/4|ENST00000634337.2:n.127+21704G>A|||||||rs1383404615||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER||ENSG00000230021|Transcript|ENST00000635509|processed_transcript||1/3|ENST00000635509.2:n.100+21704G>A|||||||rs1383404615||-1||SNV||||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000651411|lncRNA||||||||||rs1383404615|694|1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000655384|lncRNA|2/2||ENST00000655384.1:n.1578C>T||1578|||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000655765|lncRNA|3/3||ENST00000655765.1:n.1841C>T||1841|||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000656571|lncRNA||3/4|ENST00000656571.1:n.660+1126C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000657896|lncRNA||2/3|ENST00000657896.1:n.638-1251C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000658648|lncRNA||3/4|ENST00000658648.1:n.666+1126C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000665719|lncRNA||3/4|ENST00000665719.1:n.776+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000666217|lncRNA||3/3|ENST00000666217.1:n.776+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000667728|lncRNA|2/2||ENST00000667728.1:n.1480C>T||1480|||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000669749|lncRNA||2/3|ENST00000669749.1:n.589-1251C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01409|ENSG00000237491|Transcript|ENST00000670700|lncRNA||3/4|ENST00000670700.1:n.830+1000C>T|||||||rs1383404615||1||SNV|HGNC|HGNC:50701|||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:8,2:0.286:10:2,1:2,0:4,1:4,4,1,1
chr1	874082	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=37,10|7,0;DP=61;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=195,280;MMQ=60,60;MPOS=6;POPAF=7.3;ROQ=22;TLOD=16.57;CSQ=T|non_coding_transcript_exon_variant|MODIFIER|TUBB8P11|ENSG00000234711|Transcript|ENST00000415481|unprocessed_pseudogene|1/1||ENST00000415481.1:n.791C>T||791|||||||1||SNV|HGNC|HGNC:32337|YES||||||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000427857|lncRNA||2/2|ENST00000427857.1:n.173+958G>A|||||||||-1||SNV|HGNC|HGNC:27635||||3|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000432963|lncRNA|||||||||||3881|-1||SNV|HGNC|HGNC:27635||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000446136|lncRNA||2/2|ENST00000446136.1:n.1202+30G>A|||||||||-1||SNV|HGNC|HGNC:27635|YES|||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER||ENSG00000283040|Transcript|ENST00000635557|transcribed_unprocessed_pseudogene|||||||||||447|-1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:47,7:0.148:54:25,4:17,2:42,7:37,10,7,0
chr1	874370	.	AGG	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=30,69|2,4;DP=113;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=114,164;MMQ=60,60;MPOS=22;POPAF=7.3;ROQ=93;RPA=6,4;RU=G;STR;STRQ=93;TLOD=9.37;CSQ=-|downstream_gene_variant|MODIFIER|TUBB8P11|ENSG00000234711|Transcript|ENST00000415481|unprocessed_pseudogene|||||||||||22|1||deletion|HGNC|HGNC:32337|YES||||||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000427857|lncRNA||2/2|ENST00000427857.1:n.173+668_173+669del|||||||||-1||deletion|HGNC|HGNC:27635||||3|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000432963|lncRNA|||||||||||4170|-1||deletion|HGNC|HGNC:27635||||2|||||||||||||||||||||||||||||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|FAM41C|ENSG00000230368|Transcript|ENST00000446136|lncRNA|2/3||ENST00000446136.1:n.942_943del||942-943|||||||-1||deletion|HGNC|HGNC:27635|YES|||1|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER||ENSG00000283040|Transcript|ENST00000635557|transcribed_unprocessed_pseudogene|||||||||||157|-1||deletion|||YES||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:99,6:0.058:105:18,4:27,0:80,4:30,69,2,4
chr1	898145	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=25,5|3,0;DP=39;ECNT=1;GERMQ=56;MBQ=37,37;MFRL=118,103;MMQ=60,50;MPOS=3;POPAF=4.31;ROQ=12;TLOD=7.46;CSQ=T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918361|promoter_flanking_region||||||||||rs1049059485||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|intergenic_variant|MODIFIER|||||||||||||||rs1049059485||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:30,3:0.127:33:14,1:12,2:26,3:25,5,3,0
chr1	918937	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,143;MMQ=60,60;MPOS=26;POPAF=7.3;ROQ=10;TLOD=3.88;CSQ=A|downstream_gene_variant|MODIFIER||ENSG00000241180|Transcript|ENST00000398216|lncRNA||||||||||rs570906278|3966|1||SNV|||YES|||3||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000417705|lncRNA||1/3|ENST00000417705.1:n.359-22C>T|||||||rs570906278||-1||SNV|HGNC|HGNC:53933|YES|||3||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|upstream_gene_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000432961|retained_intron||||||||||rs570906278|403|-1||SNV|HGNC|HGNC:53933||||2||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000230699|Transcript|ENST00000448179|lncRNA||||||||||rs570906278|3989|1||SNV|||YES|||2||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000272438|Transcript|ENST00000607769|lncRNA||||||||||rs570906278|2961|1||SNV|||YES|||4||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|non_coding_transcript_exon_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000609207|retained_intron|1/1||ENST00000609207.1:n.2080C>T||2080|||||rs570906278||-1||SNV|HGNC|HGNC:53933||||||||||||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||||||||||rs570906278|4986|1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||||||||||rs570906278|4986|1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665||||||||0.0002|0.0008|0|0|0|0||||||||||||0.0008|AFR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,0,1
chr1	924751	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=90,93|1,3;DP=189;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=128,123;MMQ=60,60;MPOS=6;POPAF=7.3;ROQ=25;TLOD=9.94;CSQ=A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|||||||||||980|1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|||||||||||399|1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000609207|retained_intron|||||||||||3735|-1||SNV|HGNC|HGNC:53933|||||||||||||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding|1/14||ENST00000616016.5:c.320C>A|ENSP00000478421.2:p.Pro107Gln|829|320|107|P/Q|cCg/cAg|||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||deleterious_low_confidence(0)|probably_damaging(0.999)|PROSITE_profiles:PS50864&Superfamily:SSF63763||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding|||||||||||1191|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding|||||||||||1191|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding|||||||||||1191|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding|1/14||ENST00000618323.5:c.320C>A|ENSP00000480678.2:p.Pro107Gln|829|320|107|P/Q|cCg/cAg|||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||deleterious_low_confidence(0)|probably_damaging(0.999)|PROSITE_profiles:PS50864&Superfamily:SSF63763||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding|||||||||||1191|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding|||||||||||1191|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000105|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:183,4:0.024:187:67,1:74,2:159,3:0|1:924751_C_A:924751:90,93,1,3
chr1	924754	.	T	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=95,94|1,3;DP=195;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=128,123;MMQ=60,60;MPOS=3;POPAF=7.3;ROQ=31;TLOD=9.89;CSQ=G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|||||||||||977|1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|||||||||||396|1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000609207|retained_intron|||||||||||3738|-1||SNV|HGNC|HGNC:53933|||||||||||||||||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding|1/14||ENST00000616016.5:c.323T>G|ENSP00000478421.2:p.Leu108Arg|832|323|108|L/R|cTg/cGg|||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||deleterious_low_confidence(0.01)|possibly_damaging(0.561)|PROSITE_profiles:PS50864&Superfamily:SSF63763||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding|||||||||||1188|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding|||||||||||1188|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding|||||||||||1188|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,G|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding|1/14||ENST00000618323.5:c.323T>G|ENSP00000480678.2:p.Leu108Arg|832|323|108|L/R|cTg/cGg|||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||deleterious_low_confidence(0.01)|possibly_damaging(0.561)|PROSITE_profiles:PS50864&Superfamily:SSF63763||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding|||||||||||1188|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding|||||||||||1188|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000105|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:189,4:0.024:193:70,1:77,2:164,3:0|1:924751_C_A:924751:95,94,1,3
chr1	925895	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=119,49|4,2;DP=182;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=129,127;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=8;TLOD=5.14;CSQ=T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||||||||||rs199884417|4417|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||1/13|ENST00000342066.8:c.-20-27C>T|||||||rs199884417||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3|||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding||1/4|ENST00000437963.5:c.-20-27C>T|||||||rs199884417||1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|LINC02593|ENSG00000223764|Transcript|ENST00000609207|retained_intron||||||||||rs199884417|4879|-1||SNV|HGNC|HGNC:53933||||||||||||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||1/13|ENST00000616016.5:c.518-27C>T|||||||rs199884417||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||||||||||rs199884417|47|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||||||||||rs199884417|47|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||||||||||rs199884417|47|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||1/13|ENST00000618323.5:c.518-27C>T|||||||rs199884417||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||||||||||rs199884417|47|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||||||||||rs199884417|47|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000105|promoter||||||||||rs199884417||||SNV||||||||||||||||||||0.0002|0.0008|0|0|0|0|||4.062e-06|6.238e-05|0|0|0|0|0|0|0|0.0008|AFR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:168,6:0.029:174:61,1:62,2:137,4:119,49,4,2
chr1	930282	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=163,272|2,7;DP=457;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=123,104;MMQ=60,60;MPOS=7;POPAF=3.05;ROQ=12;TLOD=14.11;CSQ=A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||||||||||rs140751899|30|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A||||||||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|3/14||ENST00000342066.8:c.200G>A|ENSP00000342313.3:p.Arg67Gln|290|200|67|R/Q|cGg/cAg|rs140751899||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||tolerated(1)|benign(0.001)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|3/5||ENST00000437963.5:c.200G>A|ENSP00000393181.1:p.Arg67Gln|260|200|67|R/Q|cGg/cAg|rs140751899||1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B|||tolerated(0.73)|benign(0.001)|PANTHER:PTHR12247:SF67&PANTHER:PTHR12247&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding|3/14||ENST00000616016.5:c.737G>A|ENSP00000478421.2:p.Arg246Gln|1246|737|246|R/Q|cGg/cAg|rs140751899||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||tolerated_low_confidence(1)|benign(0.019)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding|2/11||ENST00000616125.5:c.200G>A|ENSP00000484643.1:p.Arg67Gln|200|200|67|R/Q|cGg/cAg|rs140751899||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||tolerated(1)|benign(0.005)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding|2/13||ENST00000617307.5:c.200G>A|ENSP00000482090.2:p.Arg67Gln|200|200|67|R/Q|cGg/cAg|rs140751899||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||tolerated(1)|benign(0.019)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding|2/10||ENST00000618181.5:c.200G>A|ENSP00000480870.1:p.Arg67Gln|200|200|67|R/Q|cGg/cAg|rs140751899||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||tolerated(1)|benign(0.005)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding|3/14||ENST00000618323.5:c.737G>A|ENSP00000480678.2:p.Arg246Gln|1246|737|246|R/Q|cGg/cAg|rs140751899||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||tolerated_low_confidence(1)|benign(0.019)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding|2/12||ENST00000618779.5:c.200G>A|ENSP00000484256.1:p.Arg67Gln|200|200|67|R/Q|cGg/cAg|rs140751899||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||tolerated(0.99)|benign(0.014)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||,A|missense_variant|MODERATE|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding|2/13||ENST00000622503.5:c.200G>A|ENSP00000482138.1:p.Arg67Gln|200|200|67|R/Q|cGg/cAg|rs140751899||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||tolerated(1)|benign(0.014)|PANTHER:PTHR12247&PANTHER:PTHR12247:SF67&MobiDB_lite:mobidb-lite|||0.0008|0.0023|0.0014|0|0|0|0.00433|0|0.0002572|0.00371|5.961e-05|0|0|0|1.872e-05|0.0001734|3.428e-05|0.00433|AA|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:435,9:0.023:444:157,4:167,2:342,7:163,272,2,7
chr1	930911	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=32,6|4,0;DP=43;ECNT=2;GERMQ=72;MBQ=37,37;MFRL=166,248;MMQ=60,60;MPOS=4;POPAF=4.61;ROQ=9;TLOD=10.35;CSQ=T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||1/11|ENST00000341065.8:c.26-128C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||3/13|ENST00000342066.8:c.255-128C>T|||||||rs1263233887&COSV59706160||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3|||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding||3/4|ENST00000437963.5:c.255-128C>T|||||||rs1263233887&COSV59706160||1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||3/13|ENST00000616016.5:c.792-128C>T|||||||rs1263233887&COSV59706160||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||2/10|ENST00000616125.5:c.255-128C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||2/12|ENST00000617307.5:c.255-128C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||2/9|ENST00000618181.5:c.254+575C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||3/13|ENST00000618323.5:c.792-128C>T|||||||rs1263233887&COSV59706160||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||2/11|ENST00000618779.5:c.255-128C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24||||||||||||||||||||||||||||0&1|0&1||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||2/12|ENST00000622503.5:c.255-128C>T|||||||rs1263233887&COSV59706160||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D||||||||||||||||||||||||||||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:38,4:0.131:42:8,3:24,1:32,4:32,6,4,0
chr1	935902	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=56,193|1,5;DP=269;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=133,156;MMQ=60,60;MPOS=4;POPAF=7.3;ROQ=17;TLOD=9.5;CSQ=A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||3/11|ENST00000341065.8:c.201+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||5/13|ENST00000342066.8:c.430+6G>A|||||||||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|||||||||||109|1|cds_end_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding|||||||||||3373|1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript|||||||||||4444|1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||5/13|ENST00000616016.5:c.967+6G>A|||||||||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||4/10|ENST00000616125.5:c.430+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||4/12|ENST00000617307.5:c.430+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||3/9|ENST00000618181.5:c.379+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||5/13|ENST00000618323.5:c.967+6G>A|||||||||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||4/11|ENST00000618779.5:c.430+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,A|splice_donor_region_variant&intron_variant|LOW|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||4/12|ENST00000622503.5:c.430+6G>A|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918369|promoter_flanking_region||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918370|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:249,6:0.026:255:99,3:104,2:225,5:56,193,1,5
chr1	939602	.	TG	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,1|1,2;DP=4;ECNT=2;GERMQ=18;MBQ=37,20;MFRL=171,185;MMQ=60,60;MPOS=36;POPAF=7.3;ROQ=93;RPA=4,3;RU=G;STR;STRQ=93;TLOD=5.2;CSQ=-|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|||||||||||4600|-1||deletion|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||5/11|ENST00000341065.8:c.429+194del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||7/13|ENST00000342066.8:c.706+146del|||||||||1||deletion|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000437963|protein_coding|||||||||||3810|1|cds_end_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000393181||Q5SV95.92|UPI000155D47B|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||1/6|ENST00000455979.1:c.186+146del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||||||||2563|1||deletion|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||||||||2500|1||deletion|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron|||||||||||1473|1||deletion|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|||||||||||4602|-1||deletion|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript|||||||||||743|1||deletion|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|||||||||||4601|-1||deletion|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||7/13|ENST00000616016.5:c.1195+194del|||||||||1||deletion|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||6/10|ENST00000616125.5:c.661+194del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||6/12|ENST00000617307.5:c.709+146del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||5/9|ENST00000618181.5:c.610+194del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||7/13|ENST00000618323.5:c.1198+194del|||||||||1||deletion|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||5/11|ENST00000618779.5:c.520+477del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||6/12|ENST00000622503.5:c.709+146del|||||||||1|cds_start_NF|deletion|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:1,3:0.604:4:0,1:0,0:1,2:0,1,1,2
chr1	941365	.	T	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=7,42|0,4;DP=53;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=146,215;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=32;TLOD=9.78;CSQ=C|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|||||||||||2838|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||6/11|ENST00000341065.8:c.592+59T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||8/13|ENST00000342066.8:c.869+59T>C|||||||||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||2/6|ENST00000455979.1:c.349+59T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||||||||801|1||SNV|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||||||||738|1||SNV|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron||1/3|ENST00000474461.1:n.231+59T>C|||||||||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|||||||||||2840|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript||2/2|ENST00000478729.1:n.280+59T>C|||||||||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|||||||||||2839|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript|||||||||||3954|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||8/13|ENST00000616016.5:c.1358+59T>C|||||||||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||6/10|ENST00000616125.5:c.662-1045T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||7/12|ENST00000617307.5:c.872+59T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||5/9|ENST00000618181.5:c.611-1045T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||8/13|ENST00000618323.5:c.1361+59T>C|||||||||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||6/11|ENST00000618779.5:c.683+59T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||7/12|ENST00000622503.5:c.872+59T>C|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918373|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164803|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,C|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525353187|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0240|13|N|-0.003|GCM1::MAX,C|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00494446741|||||||||||||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0597|12|N|0.002|TFAP2C::MAX,C|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524163977|||||||||||||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0401|7|Y|-0.009|MYBL1::MAX,C|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00321727920|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0238|1|N|0.006|GCM1::MAX,C|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524763170|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0382|15|N|-0.017|MGA::DLX3	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:49,4:0.102:53:18,2:23,2:43,4:7,42,0,4
chr1	941507	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,258;MMQ=60,60;MPOS=23;POPAF=7.3;ROQ=6;TLOD=3.88;CSQ=T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||||||||||rs1450130251|2696|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||6/11|ENST00000341065.8:c.592+201C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||8/13|ENST00000342066.8:c.869+201C>T|||||||rs1450130251||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||2/6|ENST00000455979.1:c.349+201C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron||||||||||rs1450130251|659|1||SNV|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron||||||||||rs1450130251|596|1||SNV|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron||1/3|ENST00000474461.1:n.231+201C>T|||||||rs1450130251||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||||||||||rs1450130251|2698|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript||2/2|ENST00000478729.1:n.280+201C>T|||||||rs1450130251||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron||||||||||rs1450130251|2697|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript||||||||||rs1450130251|3812|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||8/13|ENST00000616016.5:c.1358+201C>T|||||||rs1450130251||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||6/10|ENST00000616125.5:c.662-903C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||7/12|ENST00000617307.5:c.872+201C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||5/9|ENST00000618181.5:c.611-903C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||8/13|ENST00000618323.5:c.1361+201C>T|||||||rs1450130251||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||6/11|ENST00000618779.5:c.683+201C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||7/12|ENST00000622503.5:c.872+201C>T|||||||rs1450130251||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918373|CTCF_binding_site||||||||||rs1450130251||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164803|promoter||||||||||rs1450130251||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522333390|||||||||||rs1450130251||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0596|11|N|-0.036|TFAP2C::MAX	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,0:0,1:0,0,0,1
chr1	942032	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=5,0|2,0;DP=7;ECNT=2;GERMQ=30;MBQ=37,37;MFRL=157,188;MMQ=60,60;MPOS=8;POPAF=7.3;ROQ=18;TLOD=6.13;CSQ=T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|||||||||||2171|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||6/11|ENST00000341065.8:c.593-104C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||8/13|ENST00000342066.8:c.870-104C>T|||||||||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||2/6|ENST00000455979.1:c.350-104C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||||||||134|1||SNV|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||||||||71|1||SNV|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron||1/3|ENST00000474461.1:n.232-104C>T|||||||||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|||||||||||2173|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript||2/2|ENST00000478729.1:n.281-104C>T|||||||||1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|||||||||||2172|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript|||||||||||3287|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||8/13|ENST00000616016.5:c.1359-104C>T|||||||||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||6/10|ENST00000616125.5:c.662-378C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||7/12|ENST00000617307.5:c.873-104C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||5/9|ENST00000618181.5:c.611-378C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||8/13|ENST00000618323.5:c.1362-104C>T|||||||||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||6/11|ENST00000618779.5:c.684-104C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||7/12|ENST00000622503.5:c.873-104C>T|||||||||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164803|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:5,2:0.333:7:4,1:1,1:5,2:5,0,2,0
chr1	943587	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=7,1|3,0;DP=11;ECNT=2;GERMQ=6;MBQ=37,37;MFRL=210,152;MMQ=60,60;MPOS=8;POPAF=4.61;ROQ=19;TLOD=9.43;CSQ=T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||||||||||rs902420508|616|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||10/11|ENST00000341065.8:c.1413-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||12/13|ENST00000342066.8:c.1690-111C>T|||||||rs902420508||1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||6/6|ENST00000455979.1:c.1170-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron||||||||||rs902420508|695|1||SNV|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron||||||||||rs902420508|785|1||SNV|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron||||||||||rs902420508|593|1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||||||||||rs902420508|618|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript||||||||||rs902420508|1414|1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron||||||||||rs902420508|617|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript||||||||||rs902420508|1732|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||12/13|ENST00000616016.5:c.2179-111C>T|||||||rs902420508||1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||9/10|ENST00000616125.5:c.1366-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||11/12|ENST00000617307.5:c.1693-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||8/9|ENST00000618181.5:c.1315-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||12/13|ENST00000618323.5:c.2182-111C>T|||||||rs902420508||1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||10/11|ENST00000618779.5:c.1504-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||11/12|ENST00000622503.5:c.1693-111C>T|||||||rs902420508||1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918374|CTCF_binding_site||||||||||rs902420508||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164803|promoter||||||||||rs902420508||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:8,3:0.338:11:6,1:0,2:7,3:7,1,3,0
chr1	945622	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=50,90|5,3;DP=152;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=131,170;MMQ=54,60;MPOS=69;POPAF=7.3;ROQ=18;TLOD=12.73;CSQ=T|missense_variant|MODERATE|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|17/19||ENST00000327044.7:c.1949G>A|ENSP00000317992.6:p.Arg650Gln|1965|1949|650|R/Q|cGa/cAa|rs775649472&COSV58986206||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||deleterious(0)|probably_damaging(0.984)|Superfamily:SSF48371&PANTHER:PTHR12687&PANTHER:PTHR12687:SF10|||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding||||||||||rs775649472&COSV58986206|1047|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding||||||||||rs775649472&COSV58986206|1048|1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3|||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding||||||||||rs775649472&COSV58986206|1363|1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron||||||||||rs775649472&COSV58986206|2730|1||SNV|HGNC|HGNC:28706||||2||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron||||||||||rs775649472&COSV58986206|2820|1||SNV|HGNC|HGNC:28706||||3||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron||||||||||rs775649472&COSV58986206|2628|1||SNV|HGNC|HGNC:28706||||5||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|15/17||ENST00000477976.5:n.3396G>A||3396|||||rs775649472&COSV58986206||-1||SNV|HGNC|HGNC:24517||||5||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript||||||||||rs775649472&COSV58986206|3449|1||SNV|HGNC|HGNC:28706||||5||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron|3/5||ENST00000483767.5:n.805G>A||805|||||rs775649472&COSV58986206||-1||SNV|HGNC|HGNC:24517||||2||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript||||||||||rs775649472&COSV58986206|60|-1||SNV|HGNC|HGNC:24517||||5||||||||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding||||||||||rs775649472&COSV58986206|1048|1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding||||||||||rs775649472&COSV58986206|1469|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding||||||||||rs775649472&COSV58986206|1469|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding||||||||||rs775649472&COSV58986206|1469|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding||||||||||rs775649472&COSV58986206|1048|1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding||||||||||rs775649472&COSV58986206|1469|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding||||||||||rs775649472&COSV58986206|1469|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D||||||||||||||||7.159e-05|0|0.0004628|0|0|0|1.759e-05|0|0|0.0004628|gnomAD_AMR||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:140,8:0.05:148:59,2:52,3:113,5:50,90,5,3
chr1	946068	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=8,3|2,0;DP=20;ECNT=1;GERMQ=45;MBQ=20,37;MFRL=154,167;MMQ=60,60;MPOS=4;POPAF=7.3;ROQ=3;TLOD=5.66;CSQ=T|intron_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||16/18|ENST00000327044.7:c.1917+105G>A|||||||||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000341065|protein_coding|||||||||||1493|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000349216||H7BY14.47|UPI000155D47A|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000342066|protein_coding|||||||||||1494|1||SNV|HGNC|HGNC:28706||||5||CCDS2.2|ENSP00000342313|Q96NU1.134||UPI0000D61E04|Q96NU1-3||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000455979|protein_coding|||||||||||1809|1|cds_start_NF|SNV|HGNC|HGNC:28706||||2|||ENSP00000412228||H7C3J6.47|UPI000155D479|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000464948|retained_intron|||||||||||3176|1||SNV|HGNC|HGNC:28706||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000466827|retained_intron|||||||||||3266|1||SNV|HGNC|HGNC:28706||||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000474461|retained_intron|||||||||||3074|1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||14/16|ENST00000477976.5:n.3364+105G>A|||||||||-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000478729|processed_transcript|||||||||||3895|1||SNV|HGNC|HGNC:28706||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000483767|retained_intron||2/4|ENST00000483767.5:n.773+105G>A|||||||||-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000496938|processed_transcript|||||||||||506|-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616016|protein_coding|||||||||||1494|1||SNV|HGNC|HGNC:28706|YES|NM_001385641.1||5|A2||ENSP00000478421||I7G285.48|UPI0015DA7BD7|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000616125|protein_coding|||||||||||1915|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484643||A0A087X223.34|UPI0004E4CACB|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000617307|protein_coding|||||||||||1915|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482090||A0A087WYU3.31|UPI00194D500F|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618181|protein_coding|||||||||||1915|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000480870||A0A087WXB3.31|UPI0004E4CAA9|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618323|protein_coding|||||||||||1494|1||SNV|HGNC|HGNC:28706||||5|P5||ENSP00000480678||A0A087WX24.28|UPI0015DAE665|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000618779|protein_coding|||||||||||1915|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000484256||A0A087X1J5.31|UPI0004E4CB24|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SAMD11|ENSG00000187634|Transcript|ENST00000622503|protein_coding|||||||||||1915|1|cds_start_NF|SNV|HGNC|HGNC:28706||||5|||ENSP00000482138||A0A087WYW1.41|UPI0004E4CA1D|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:11,2:0.264:13:0,2:7,0:7,2:8,3,2,0
chr1	956211	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=47,161|2,2;DP=213;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=136,191;MMQ=60,60;MPOS=68;POPAF=3.12;ROQ=6;TLOD=3.46;CSQ=T|missense_variant|MODERATE|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding|5/19||ENST00000327044.7:c.491G>A|ENSP00000317992.6:p.Arg164His|507|491|164|R/H|cGc/cAc|rs138672231&COSV58533801||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||tolerated(0.79)|benign(0)|Superfamily:SSF48371&PANTHER:PTHR12687&PANTHER:PTHR12687:SF10|||0.0006|0|0|0|0.001|0.002|0|0.001977|0.001309|0.0001852|0.0002893|0.005875|5.44e-05|0.0005147|0.001192|0.001145|0.003332|0.005875|gnomAD_ASJ||0&1|0&1||||||,T|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding||||||||||rs138672231&COSV58533801|4373|1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0||||||||0.0006|0|0|0|0.001|0.002|0|0.001977|0.001309|0.0001852|0.0002893|0.005875|5.44e-05|0.0005147|0.001192|0.001145|0.003332|0.005875|gnomAD_ASJ||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000469563|retained_intron||||||||||rs138672231&COSV58533801|2035|-1||SNV|HGNC|HGNC:24517||||2||||||||||||||0.0006|0|0|0|0.001|0.002|0|0.001977|0.001309|0.0001852|0.0002893|0.005875|5.44e-05|0.0005147|0.001192|0.001145|0.003332|0.005875|gnomAD_ASJ||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron|3/17||ENST00000477976.5:n.1497G>A||1497|||||rs138672231&COSV58533801||-1||SNV|HGNC|HGNC:24517||||5||||||||||||||0.0006|0|0|0|0.001|0.002|0|0.001977|0.001309|0.0001852|0.0002893|0.005875|5.44e-05|0.0005147|0.001192|0.001145|0.003332|0.005875|gnomAD_ASJ||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000487214|processed_transcript|5/7||ENST00000487214.1:n.560G>A||560|||||rs138672231&COSV58533801||-1||SNV|HGNC|HGNC:24517||||3||||||||||||||0.0006|0|0|0|0.001|0.002|0|0.001977|0.001309|0.0001852|0.0002893|0.005875|5.44e-05|0.0005147|0.001192|0.001145|0.003332|0.005875|gnomAD_ASJ||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:208,4:0.017:212:76,1:90,1:173,2:47,161,2,2
chr1	956311	.	C	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=3,12|1,3;DP=21;ECNT=1;GERMQ=41;MBQ=37,29;MFRL=191,241;MMQ=60,60;MPOS=25;POPAF=7.3;ROQ=34;TLOD=9.7;CSQ=G|intron_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||4/18|ENST00000327044.7:c.487-96G>C|||||||||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding|||||||||||4273|1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0|||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000469563|retained_intron|||||||||||1935|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||2/16|ENST00000477976.5:n.1493-96G>C|||||||||-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000487214|processed_transcript||4/6|ENST00000487214.1:n.556-96G>C|||||||||-1||SNV|HGNC|HGNC:24517||||3|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:15,4:0.235:19:6,2:5,1:12,3:3,12,1,3
chr1	956663	.	A	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=12,1|3,0;DP=16;ECNT=1;GERMQ=42;MBQ=37,37;MFRL=207,180;MMQ=60,60;MPOS=24;POPAF=7.3;ROQ=27;TLOD=8.67;CSQ=G|intron_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||4/18|ENST00000327044.7:c.486+231T>C|||||||||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding|||||||||||3921|1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212|retained_intron|||||||||||4786|1||SNV|HGNC|HGNC:24023||||1|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000469563|retained_intron|||||||||||1583|-1||SNV|HGNC|HGNC:24517||||2|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||2/16|ENST00000477976.5:n.1492+231T>C|||||||||-1||SNV|HGNC|HGNC:24517||||5|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000487214|processed_transcript||4/6|ENST00000487214.1:n.555+231T>C|||||||||-1||SNV|HGNC|HGNC:24517||||3|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:13,3:0.235:16:3,1:9,2:12,3:12,1,3,0
chr1	963011	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=3,12|2,0;DP=21;ECNT=2;GERMQ=28;MBQ=37,37;MFRL=210,173;MMQ=60,60;MPOS=5;POPAF=4.61;ROQ=2;TLOD=5.09;CSQ=T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||||||||||rs759147179|3755|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|intron_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding||6/11|ENST00000338591.8:c.1042+94C>T|||||||rs759147179||1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding||||||||||rs759147179|3491|1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3|||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding||||||||||rs759147179|3491|1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2|||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding||||||||||rs759147179|3471|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1|||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212|retained_intron||||||||||rs759147179|533|1||SNV|HGNC|HGNC:24023||||1||||||||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300|nonsense_mediated_decay||1/5|ENST00000466300.1:c.192-21C>T|||||||rs759147179||1|cds_start_NF|SNV|HGNC|HGNC:24023||||3|||ENSP00000463694||J3QLT4.38|UPI000268AE1E||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000469563|retained_intron||||||||||rs759147179|3755|-1||SNV|HGNC|HGNC:24517||||2||||||||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||||||||||rs759147179|4553|-1||SNV|HGNC|HGNC:24517||||5||||||||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067|retained_intron||||||||||rs759147179|541|1||SNV|HGNC|HGNC:24023||||2||||||||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000487214|processed_transcript||||||||||rs759147179|3702|-1||SNV|HGNC|HGNC:24517||||3||||||||||||||||||||||1.251e-05|0|0|0|0|0|3.059e-05|0|0|3.059e-05|gnomAD_NFE|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:15,2:0.174:17:7,0:6,2:13,2:0|1:963011_C_T:963011:3,12,2,0
chr1	963446	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=103,123|5,6;DP=241;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=117,161;MMQ=60,60;MPOS=6;POPAF=7.3;ROQ=9;TLOD=19.6;CSQ=A|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||||||||||rs202077085&COSV58531272|4190|-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|missense_variant|MODERATE|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding|8/12||ENST00000338591.8:c.1297G>A|ENSP00000343930.3:p.Ala433Thr|1407|1297|433|A/T|Gcc/Acc|rs202077085&COSV58531272||1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0|||tolerated(0.08)|benign(0.006)|Gene3D:2.120.10.80&Pfam:PF01344&PANTHER:PTHR24412&PANTHER:PTHR24412:SF454&SMART:SM00612&Superfamily:SSF50965&PIRSF:PIRSF037037&PDB-ENSP_mappings:6hrl.A&PDB-ENSP_mappings:6hrl.B|||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding||||||||||rs202077085&COSV58531272|3056|1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3|||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding||||||||||rs202077085&COSV58531272|3056|1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2|||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding||||||||||rs202077085&COSV58531272|3036|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1|||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212|retained_intron||||||||||rs202077085&COSV58531272|968|1||SNV|HGNC|HGNC:24023||||1||||||||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300|nonsense_mediated_decay|3/6||ENST00000466300.1:c.*60G>A||523|||||rs202077085&COSV58531272||1|cds_start_NF|SNV|HGNC|HGNC:24023||||3|||ENSP00000463694||J3QLT4.38|UPI000268AE1E||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000469563|retained_intron||||||||||rs202077085&COSV58531272|4190|-1||SNV|HGNC|HGNC:24517||||2||||||||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000477976|retained_intron||||||||||rs202077085&COSV58531272|4988|-1||SNV|HGNC|HGNC:24517||||5||||||||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067|retained_intron||||||||||rs202077085&COSV58531272|106|1||SNV|HGNC|HGNC:24023||||2||||||||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|NOC2L|ENSG00000188976|Transcript|ENST00000487214|processed_transcript||||||||||rs202077085&COSV58531272|4137|-1||SNV|HGNC|HGNC:24517||||3||||||||||||||0.0002|0|0|0.001|0|0|||8.023e-06|0|0|0|5.444e-05|0|8.915e-06|0|0|0.001|EAS||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:226,11:0.044:237:100,2:72,6:191,8:103,123,5,6
chr1	964969	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=201,85|2,3;DP=327;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=126,88;MMQ=60,60;MPOS=12;POPAF=4.13;ROQ=4;TLOD=5.27;CSQ=A|synonymous_variant|LOW|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding|12/12||ENST00000338591.8:c.1707G>A|ENSP00000343930.3:p.Thr569%3D|1817|1707|569|T|acG/acA|rs372754678||1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0|||||Gene3D:2.120.10.80&Pfam:PF01344&PANTHER:PTHR24412&PANTHER:PTHR24412:SF454&SMART:SM00612&Superfamily:SSF50965&PIRSF:PIRSF037037&PDB-ENSP_mappings:6hrl.A&PDB-ENSP_mappings:6hrl.B|||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding||||||||||rs372754678|1533|1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3|||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding||||||||||rs372754678|1533|1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2|||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding||||||||||rs372754678|1513|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1|||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212|retained_intron||||||||||rs372754678|2491|1||SNV|HGNC|HGNC:24023||||1||||||||||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300|nonsense_mediated_decay||||||||||rs372754678|439|1|cds_start_NF|SNV|HGNC|HGNC:24023||||3|||ENSP00000463694||J3QLT4.38|UPI000268AE1E||||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||,A|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067|retained_intron||||||||||rs372754678|805|1||SNV|HGNC|HGNC:24023||||2||||||||||||||||||||0|0.0001164|3.72e-05|0|5.881e-05|0|0|0|5.561e-05|0|3.318e-05|0.0001164|EA|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:286,5:0.016:291:120,2:114,1:239,3:201,85,2,3
chr1	966767	.	C	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=91,169|3,5;DP=285;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=115,163;MMQ=60,60;MPOS=11;POPAF=7.3;ROQ=51;TLOD=10.89;CSQ=G|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000338591|protein_coding|||||||||||1048|1||SNV|HGNC|HGNC:24023|YES|NM_198317.3||1|P1|CCDS30550.1|ENSP00000343930|Q6TDP4.141||UPI00001DFBF0|||||||||||||||||||||||||||||||||||,G|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding|2/15||ENST00000379407.7:c.147C>G|ENSP00000368717.2:p.Ala49%3D|177|147|49|A|gcC/gcG|||1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3||||PANTHER:PTHR46882||||||||||||||||||||||||||||||,G|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding|2/15||ENST00000379409.6:c.147C>G|ENSP00000368719.2:p.Ala49%3D|177|147|49|A|gcC/gcG|||1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2||||PANTHER:PTHR46882||||||||||||||||||||||||||||||,G|synonymous_variant|LOW|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding|2/16||ENST00000379410.8:c.147C>G|ENSP00000368720.3:p.Ala49%3D|197|147|49|A|gcC/gcG|||1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1||||PANTHER:PTHR46882||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000463212|retained_intron|||||||||||4289|1||SNV|HGNC|HGNC:24023||||1|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000466300|nonsense_mediated_decay|||||||||||2237|1|cds_start_NF|SNV|HGNC|HGNC:24023||||3|||ENSP00000463694||J3QLT4.38|UPI000268AE1E|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000480267|retained_intron|||||||||||4108|1||SNV|HGNC|HGNC:25284||||3|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|KLHL17|ENSG00000187961|Transcript|ENST00000481067|retained_intron|||||||||||2603|1||SNV|HGNC|HGNC:24023||||2|||||||||||||||||||||||||||||||||||||||||,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000112|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,G|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00042468395|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0114|11|N|-0.010|ETV2::FOXI1&ELK1::FOXI1&ERF::FOXI1&FOXO1::ELF1&FOXO1::ELK1&FLI1::FOXI1&ETV5::FOXI1	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:260,8:0.026:268:121,2:100,3:227,5:91,169,3,5
chr1	972943	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=141,108|3,1;DP=266;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=123,79;MMQ=60,60;MPOS=19;POPAF=2.06;ROQ=4;TLOD=4.78;CSQ=A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding||||||||||rs61732689&COSV58022189|2261|-1||SNV|HGNC|HGNC:28208||||2|A2||ENSP00000343864|Q5SV97.102||UPI000022DAF4|Q5SV97-3|||||||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding|11/15||ENST00000379407.7:c.1121G>A|ENSP00000368717.2:p.Arg374His|1151|1121|374|R/H|cGc/cAc|rs61732689&COSV58022189||1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3||tolerated(0.36)|benign(0.005)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding|10/15||ENST00000379409.6:c.1241G>A|ENSP00000368719.2:p.Arg414His|1271|1241|414|R/H|cGc/cAc|rs61732689&COSV58022189||1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2||tolerated(0.43)|benign(0.007)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding|11/16||ENST00000379410.8:c.1085G>A|ENSP00000368720.3:p.Arg362His|1135|1085|362|R/H|cGc/cAc|rs61732689&COSV58022189||1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1||tolerated(0.43)|benign(0.003)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding||||||||||rs61732689&COSV58022189|2262|-1||SNV|HGNC|HGNC:28208|YES|||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97.102||UPI0003E30FA7|Q5SV97-1|||||||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000479361|retained_intron||||||||||rs61732689&COSV58022189|2262|-1||SNV|HGNC|HGNC:28208||||1||||||||||||||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000480267|retained_intron||||||||||rs61732689&COSV58022189|1420|1||SNV|HGNC|HGNC:25284||||3||||||||||||||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000491024|protein_coding||||||||||rs61732689&COSV58022189|569|1|cds_start_NF|SNV|HGNC|HGNC:25284||||3|||ENSP00000462558||J3KSM5.40|UPI000268AE1F||||||||0.0128|0.0461|0.0043|0|0|0|0.03755|0.0005858|0.002653|0.04427|0.001686|0|7.637e-05|6.334e-05|7.056e-05|0.001267|0.000162|0.0461|AFR||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:249,4:0.019:253:111,2:92,1:208,3:141,108,3,1
chr1	974495	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=98,66|3,5;DP=180;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=130,124;MMQ=60,60;MPOS=2;POPAF=2.85;ROQ=15;TLOD=16.47;CSQ=A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding||||||||||rs148853412|709|-1||SNV|HGNC|HGNC:28208||||2|A2||ENSP00000343864|Q5SV97.102||UPI000022DAF4|Q5SV97-3|||||||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379407|protein_coding|15/15||ENST00000379407.7:c.1651G>A|ENSP00000368717.2:p.Glu551Lys|1681|1651|551|E/K|Gag/Aag|rs148853412||1||SNV|HGNC|HGNC:25284||||1|A2|CCDS53256.1|ENSP00000368717|Q494U1.126||UPI00005764FF|Q494U1-3||tolerated_low_confidence(1)|benign(0.003)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite|||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379409|protein_coding|15/15||ENST00000379409.6:c.1912G>A|ENSP00000368719.2:p.Glu638Lys|1942|1912|638|E/K|Gag/Aag|rs148853412||1||SNV|HGNC|HGNC:25284||||2|P4||ENSP00000368719|Q494U1.126||UPI0000D61E06|Q494U1-2||tolerated(1)|benign(0.011)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite|||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding|16/16||ENST00000379410.8:c.1756G>A|ENSP00000368720.3:p.Glu586Lys|1806|1756|586|E/K|Gag/Aag|rs148853412||1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1||tolerated_low_confidence(1)|benign(0.001)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite|||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding||||||||||rs148853412|710|-1||SNV|HGNC|HGNC:28208|YES|||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97.102||UPI0003E30FA7|Q5SV97-1|||||||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|downstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000479361|retained_intron||||||||||rs148853412|710|-1||SNV|HGNC|HGNC:28208||||1||||||||||||||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000480267|retained_intron||||||||||rs148853412|2972|1||SNV|HGNC|HGNC:25284||||3||||||||||||||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||,A|missense_variant|MODERATE|PLEKHN1|ENSG00000187583|Transcript|ENST00000491024|protein_coding|4/5||ENST00000491024.1:c.451G>A|ENSP00000462558.1:p.Glu151Lys|451|451|151|E/K|Gag/Aag|rs148853412||1|cds_start_NF|SNV|HGNC|HGNC:25284||||3|||ENSP00000462558||J3KSM5.40|UPI000268AE1F|||tolerated(1)|benign(0.011)|PANTHER:PTHR46882&MobiDB_lite:mobidb-lite|||0.0018|0.0068|0|0|0|0|0.006131|0|0.0004293|0.005915|0.0002607|0|0|0|8.917e-06|0.0003289|0|0.0068|AFR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:164,8:0.047:172:66,4:74,2:144,7:98,66,3,5
chr1	980177	.	A	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=84,148|5,2;DP=255;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=138,212;MMQ=60,60;MPOS=27;POPAF=7.3;ROQ=4;TLOD=9.34;CSQ=C|missense_variant|MODERATE|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding|3/5||ENST00000341290.6:c.511T>G|ENSP00000343864.2:p.Trp171Gly|547|511|171|W/G|Tgg/Ggg|||-1||SNV|HGNC|HGNC:28208||||2|A2||ENSP00000343864|Q5SV97.102||UPI000022DAF4|Q5SV97-3||tolerated(0.5)|benign(0)|PANTHER:PTHR47282&MobiDB_lite:mobidb-lite||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000379410|protein_coding|||||||||||4312|1||SNV|HGNC|HGNC:25284|YES|NM_032129.3||1|A2|CCDS4.1|ENSP00000368720|Q494U1.126||UPI00001416D8|Q494U1-1||||||||||||||||||||||||||||||||||,C|missense_variant|MODERATE|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding|1/3||ENST00000433179.3:c.853T>G|ENSP00000414022.3:p.Trp285Gly|853|853|285|W/G|Tgg/Ggg|||-1||SNV|HGNC|HGNC:28208|YES|||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97.102||UPI0003E30FA7|Q5SV97-1||tolerated(0.41)|benign(0.003)|PANTHER:PTHR47282&MobiDB_lite:mobidb-lite||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000479361|retained_intron|||||||||||3536|-1||SNV|HGNC|HGNC:28208||||1|||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|PLEKHN1|ENSG00000187583|Transcript|ENST00000491024|protein_coding|||||||||||4312|1|cds_start_NF|SNV|HGNC|HGNC:25284||||3|||ENSP00000462558||J3KSM5.40|UPI000268AE1F|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:232,7:0.029:239:82,0:103,5:200,5:84,148,5,2
chr1	981651	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,172;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=9;TLOD=3.88;CSQ=A|intron_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding||1/4|ENST00000341290.6:c.-8+414C>T|||||||||-1||SNV|HGNC|HGNC:28208||||2|A2||ENSP00000343864|Q5SV97.102||UPI000022DAF4|Q5SV97-3||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding|||||||||||622|-1||SNV|HGNC|HGNC:28208|YES|||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97.102||UPI0003E30FA7|Q5SV97-1||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344447|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	981866	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,212;MMQ=60,60;MPOS=4;POPAF=7.3;ROQ=7;TLOD=3.87;CSQ=T|intron_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000341290|protein_coding||1/4|ENST00000341290.6:c.-8+199G>A|||||||||-1||SNV|HGNC|HGNC:28208||||2|A2||ENSP00000343864|Q5SV97.102||UPI000022DAF4|Q5SV97-3||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|PERM1|ENSG00000187642|Transcript|ENST00000433179|protein_coding|||||||||||837|-1||SNV|HGNC|HGNC:28208|YES|||5|P2|CCDS76083.1|ENSP00000414022|Q5SV97.102||UPI0003E30FA7|Q5SV97-1||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344447|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,1,0
chr1	1013876	.	G	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=24,5|2,0;DP=36;ECNT=2;GERMQ=93;MBQ=25,37;MFRL=186,184;MMQ=60,60;MPOS=15;POPAF=7.3;ROQ=6;TLOD=4.4;CSQ=T|upstream_gene_variant|MODIFIER||ENSG00000224969|Transcript|ENST00000458555|lncRNA|||||||||||683|-1||SNV|||YES|||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624652|protein_coding||2/2|ENST00000624652.1:c.-21-108G>T|||||||||1|cds_end_NF|SNV|HGNC|HGNC:4053||||3|||ENSP00000485313||A0A096LNZ9.43|UPI00053BD5BA||1|||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624697|protein_coding||2/2|ENST00000624697.4:c.-21-108G>T|||||||||1||SNV|HGNC|HGNC:4053||||3|||ENSP00000485643||A0A096LPJ4.38|UPI0004F23698||1|||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000649529|protein_coding||1/1|ENST00000649529.1:c.4-108G>T|||||||||1||SNV|HGNC|HGNC:4053|YES|NM_005101.4|||P1|CCDS6.1|ENSP00000496832|P05161.224||UPI0000048D70||1|||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164809|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:29,2:0.107:31:13,2:9,0:24,2:24,5,2,0
chr1	1014052	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=275,286|4,5;DP=610;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=125,130;MMQ=60,60;MPOS=27;POPAF=4.31;ROQ=6;TLOD=16.33;CSQ=A|upstream_gene_variant|MODIFIER||ENSG00000224969|Transcript|ENST00000458555|lncRNA||||||||||rs939961004|859|-1||SNV|||YES|||2||||||||||||||||||||||7.982e-06|0|5.787e-05|0|0|0|0|0|0|5.787e-05|gnomAD_AMR|||||||||,A|synonymous_variant|LOW|ISG15|ENSG00000187608|Transcript|ENST00000624652|protein_coding|3/3||ENST00000624652.1:c.48G>A|ENSP00000485313.1:p.Ser16%3D|274|48|16|S|tcG/tcA|rs939961004||1|cds_end_NF|SNV|HGNC|HGNC:4053||||3|||ENSP00000485313||A0A096LNZ9.43|UPI00053BD5BA||1|||Gene3D:3.10.20.90&Pfam:PF00240&PROSITE_profiles:PS50053&PANTHER:PTHR10666&PANTHER:PTHR10666:SF267&SMART:SM00213&Superfamily:SSF54236&Low_complexity_(Seg):seg|||||||||||7.982e-06|0|5.787e-05|0|0|0|0|0|0|5.787e-05|gnomAD_AMR|||||||||,A|synonymous_variant|LOW|ISG15|ENSG00000187608|Transcript|ENST00000624697|protein_coding|3/3||ENST00000624697.4:c.48G>A|ENSP00000485643.1:p.Ser16%3D|299|48|16|S|tcG/tcA|rs939961004||1||SNV|HGNC|HGNC:4053||||3|||ENSP00000485643||A0A096LPJ4.38|UPI0004F23698||1|||Gene3D:3.10.20.90&Pfam:PF00240&PROSITE_profiles:PS50053&PANTHER:PTHR10666&PANTHER:PTHR10666:SF267&SMART:SM00213&Superfamily:SSF54236&Low_complexity_(Seg):seg|||||||||||7.982e-06|0|5.787e-05|0|0|0|0|0|0|5.787e-05|gnomAD_AMR|||||||||,A|synonymous_variant|LOW|ISG15|ENSG00000187608|Transcript|ENST00000649529|protein_coding|2/2||ENST00000649529.1:c.72G>A|ENSP00000496832.1:p.Ser24%3D|149|72|24|S|tcG/tcA|rs939961004||1||SNV|HGNC|HGNC:4053|YES|NM_005101.4|||P1|CCDS6.1|ENSP00000496832|P05161.224||UPI0000048D70||1|||PDB-ENSP_mappings:1z2m.A&Gene3D:3.10.20.90&PDB-ENSP_mappings:3pse.B&PDB-ENSP_mappings:3r66.C&PDB-ENSP_mappings:3r66.D&PDB-ENSP_mappings:3rt3.B&PDB-ENSP_mappings:3sdl.C&PDB-ENSP_mappings:3sdl.D&PDB-ENSP_mappings:6bi8.C&PDB-ENSP_mappings:6bi8.D&Pfam:PF00240&PROSITE_profiles:PS50053&PANTHER:PTHR10666&PANTHER:PTHR10666:SF267&SMART:SM00213&Superfamily:SSF54236&CDD:cd01792&Low_complexity_(Seg):seg|||||||||||7.982e-06|0|5.787e-05|0|0|0|0|0|0|5.787e-05|gnomAD_AMR|||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164809|promoter||||||||||rs939961004||||SNV||||||||||||||||||||||||||||7.982e-06|0|5.787e-05|0|0|0|0|0|0|5.787e-05|gnomAD_AMR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:561,9:0.021:570:223,7:239,2:471,9:275,286,4,5
chr1	1014451	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=155,273|5,5;DP=444;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=126,69;MMQ=60,60;MPOS=17;POPAF=1.96;ROQ=8;TLOD=14.74;CSQ=T|upstream_gene_variant|MODIFIER||ENSG00000224969|Transcript|ENST00000458555|lncRNA||||||||||rs116002608&COSV65106772|1258|-1||SNV|||YES|||2||||||||||||||0.0156|0.0371|0.0029|0.0218|0.001|0.0041|0.02735|0.0009324|0.007128|0.02796|0.002525|0.00569|0.02188|0.01999|0.001507|0.007117|0.004663|0.0371|AFR|benign|0&1|1&1||||||,T|downstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624652|protein_coding||||||||||rs116002608&COSV65106772|16|1|cds_end_NF|SNV|HGNC|HGNC:4053||||3|||ENSP00000485313||A0A096LNZ9.43|UPI00053BD5BA||1||||||0.0156|0.0371|0.0029|0.0218|0.001|0.0041|0.02735|0.0009324|0.007128|0.02796|0.002525|0.00569|0.02188|0.01999|0.001507|0.007117|0.004663|0.0371|AFR|benign|0&1|1&1||||||,T|synonymous_variant|LOW|ISG15|ENSG00000187608|Transcript|ENST00000624697|protein_coding|3/3||ENST00000624697.4:c.447C>T|ENSP00000485643.1:p.Gly149%3D|698|447|149|G|ggC/ggT|rs116002608&COSV65106772||1||SNV|HGNC|HGNC:4053||||3|||ENSP00000485643||A0A096LPJ4.38|UPI0004F23698||1|||Gene3D:3.10.20.90&PROSITE_profiles:PS50053&PANTHER:PTHR10666&PANTHER:PTHR10666:SF267&Superfamily:SSF54236|||0.0156|0.0371|0.0029|0.0218|0.001|0.0041|0.02735|0.0009324|0.007128|0.02796|0.002525|0.00569|0.02188|0.01999|0.001507|0.007117|0.004663|0.0371|AFR|benign|0&1|1&1||||||,T|synonymous_variant|LOW|ISG15|ENSG00000187608|Transcript|ENST00000649529|protein_coding|2/2||ENST00000649529.1:c.471C>T|ENSP00000496832.1:p.Gly157%3D|548|471|157|G|ggC/ggT|rs116002608&COSV65106772||1||SNV|HGNC|HGNC:4053|YES|NM_005101.4|||P1|CCDS6.1|ENSP00000496832|P05161.224||UPI0000048D70||1|||PDB-ENSP_mappings:2hj8.A&Gene3D:3.10.20.90&PDB-ENSP_mappings:3r66.C&PDB-ENSP_mappings:3r66.D&PDB-ENSP_mappings:3rt3.B&PDB-ENSP_mappings:3sdl.C&PDB-ENSP_mappings:3sdl.D&PDB-ENSP_mappings:5tl6.A&PDB-ENSP_mappings:5tl6.C&PDB-ENSP_mappings:6xa9.B&PDB-ENSP_mappings:6xa9.D&PDB-ENSP_mappings:6xa9.F&PROSITE_profiles:PS50053&PANTHER:PTHR10666&PANTHER:PTHR10666:SF267&Superfamily:SSF54236|||0.0156|0.0371|0.0029|0.0218|0.001|0.0041|0.02735|0.0009324|0.007128|0.02796|0.002525|0.00569|0.02188|0.01999|0.001507|0.007117|0.004663|0.0371|AFR|benign|0&1|1&1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164809|promoter||||||||||rs116002608&COSV65106772||||SNV||||||||||||||||||||0.0156|0.0371|0.0029|0.0218|0.001|0.0041|0.02735|0.0009324|0.007128|0.02796|0.002525|0.00569|0.02188|0.01999|0.001507|0.007117|0.004663|0.0371|AFR|benign|0&1|1&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:428,10:0.022:438:168,5:169,2:353,7:155,273,5,5
chr1	1017131	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,0;MMQ=60,41;MPOS=3;POPAF=7.3;ROQ=11;TLOD=3.88;CSQ=T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|||||||||||2989|1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000224969|Transcript|ENST00000458555|lncRNA|||||||||||3938|-1||SNV|||YES|||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|||||||||||2992|1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624652|protein_coding|||||||||||2696|1|cds_end_NF|SNV|HGNC|HGNC:4053||||3|||ENSP00000485313||A0A096LNZ9.43|UPI00053BD5BA||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000624697|protein_coding|||||||||||2591|1||SNV|HGNC|HGNC:4053||||3|||ENSP00000485643||A0A096LPJ4.38|UPI0004F23698||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ISG15|ENSG00000187608|Transcript|ENST00000649529|protein_coding|||||||||||2591|1||SNV|HGNC|HGNC:4053|YES|NM_005101.4|||P1|CCDS6.1|ENSP00000496832|P05161.224||UPI0000048D70||1|||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,0,1
chr1	1033312	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;GERMQ=31;MBQ=0,37;MFRL=0,103;MMQ=60,60;MPOS=24;POPAF=7.3;ROQ=16;TLOD=3.88;CSQ=A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding||2/35|ENST00000379370.7:c.464-1965C>A|||||||||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron|||||||||||1555|1||SNV|HGNC|HGNC:329||||3||||||||1|||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding||2/38|ENST00000620552.4:c.50-1965C>A|||||||||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|||||||||||794|1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|||||||||||794|1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000125|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344466|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523824979|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0257|16|Y|-0.032|GCM2::E2F8,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525176514|||||||||||||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0084|5|Y|-0.092|E2F8,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00192354384|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0240|4|N|-0.004|GCM1::MAX,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523885447|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0497|6|N|0.031|SOX6::TBX21	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1033323	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;GERMQ=31;MBQ=0,37;MFRL=0,103;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=16;TLOD=3.88;CSQ=A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding||2/35|ENST00000379370.7:c.464-1954C>A|||||||||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron|||||||||||1544|1||SNV|HGNC|HGNC:329||||3||||||||1|||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding||2/38|ENST00000620552.4:c.50-1954C>A|||||||||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|||||||||||783|1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|||||||||||783|1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000125|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344466|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523824979|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0257|5|N|-0.033|GCM2::E2F8	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1044428	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=84,138|2,6;DP=253;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=120,134;MMQ=60,60;MPOS=5;POPAF=7.3;ROQ=18;TLOD=10.76;CSQ=A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|12/36||ENST00000379370.7:c.2243G>A|ENSP00000368678.2:p.Gly748Glu|2296|2243|748|G/E|gGa/gAa|rs758309910||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|deleterious(0.03)|probably_damaging(0.997)|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00280&Superfamily:SSF100895&CDD:cd00104|||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000466223|retained_intron||||||||||rs758309910|2773|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron||||||||||rs758309910|3031|1||SNV|HGNC|HGNC:329||||3||||||||1||||||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000478677|retained_intron||||||||||rs758309910|3047|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron||||||||||rs758309910|971|1||SNV|HGNC|HGNC:329||||3||||||||1||||||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron||||||||||rs758309910|4101|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|12/39||ENST00000620552.4:c.1829G>A|ENSP00000484607.1:p.Gly610Glu|2293|1829|610|G/E|gGa/gAa|rs758309910||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|deleterious(0)|probably_damaging(1)|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00280&Superfamily:SSF100895&CDD:cd00104|||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|11/38||ENST00000651234.1:c.1928G>A|ENSP00000499046.1:p.Gly643Glu|2378|1928|643|G/E|gGa/gAa|rs758309910||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|deleterious(0)|benign(0.021)|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00280&Superfamily:SSF100895&CDD:cd00104|||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|11/35||ENST00000652369.1:c.1928G>A|ENSP00000498543.1:p.Gly643Glu|2378|1928|643|G/E|gGa/gAa|rs758309910||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|deleterious(0)|benign(0.021)|Gene3D:3.30.60.30&Pfam:PF07648&PROSITE_profiles:PS51465&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00280&Superfamily:SSF100895&CDD:cd00104|||||||||||1.254e-05|0|0|0|0|0|2.797e-05|0|0|2.797e-05|gnomAD_NFE|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:222,8:0.033:230:100,3:73,2:181,6:84,138,2,6
chr1	1045491	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=83,124|7,7;DP=224;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=121,87;MMQ=60,60;MPOS=10;POPAF=7.3;ROQ=17;TLOD=19.45;CSQ=A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|14/36||ENST00000379370.7:c.2504G>A|ENSP00000368678.2:p.Gly835Asp|2557|2504|835|G/D|gGc/gAc|||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|deleterious(0)|probably_damaging(1)|Gene3D:2.10.25.10&Pfam:PF00053&PROSITE_patterns:PS01248&PROSITE_profiles:PS50027&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00180&Superfamily:SSF57196||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000466223|retained_intron|||||||||||1710|1||SNV|HGNC|HGNC:329||||2||||||||1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000469403|retained_intron|||||||||||4094|1||SNV|HGNC|HGNC:329||||3||||||||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000478677|retained_intron|||||||||||1984|1||SNV|HGNC|HGNC:329||||2||||||||1|||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron|1/4||ENST00000479707.1:n.93G>A||93|||||||1||SNV|HGNC|HGNC:329||||3||||||||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron|||||||||||3038|1||SNV|HGNC|HGNC:329||||2||||||||1|||||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|14/39||ENST00000620552.4:c.2090G>A|ENSP00000484607.1:p.Gly697Asp|2554|2090|697|G/D|gGc/gAc|||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|deleterious(0.03)|probably_damaging(1)|Gene3D:2.10.25.10&Pfam:PF00053&PROSITE_patterns:PS01248&PROSITE_profiles:PS50027&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00180&Superfamily:SSF57196||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|13/38||ENST00000651234.1:c.2189G>A|ENSP00000499046.1:p.Gly730Asp|2639|2189|730|G/D|gGc/gAc|||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|deleterious(0.03)|possibly_damaging(0.699)|Gene3D:2.10.25.10&Pfam:PF00053&PROSITE_patterns:PS01248&PROSITE_profiles:PS50027&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00180&Superfamily:SSF57196||||||||||||||||||||||||||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|13/35||ENST00000652369.1:c.2189G>A|ENSP00000498543.1:p.Gly730Asp|2639|2189|730|G/D|gGc/gAc|||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|deleterious(0)|possibly_damaging(0.699)|Gene3D:2.10.25.10&Pfam:PF00053&PROSITE_patterns:PS01248&PROSITE_profiles:PS50027&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00180&Superfamily:SSF57196||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:207,14:0.047:221:53,5:38,2:161,7:83,124,7,7
chr1	1047806	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=131,134|2,4;DP=282;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=130,134;MMQ=60,60;MPOS=30;POPAF=4.31;ROQ=2;TLOD=7.7;CSQ=A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|22/36||ENST00000379370.7:c.3662G>A|ENSP00000368678.2:p.Arg1221Gln|3715|3662|1221|R/Q|cGg/cAg|rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|tolerated(0.36)|benign(0.006)|Gene3D:3.30.70.960&Pfam:PF01390&PROSITE_profiles:PS50024&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00200&Superfamily:SSF82671|||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000461111|retained_intron||||||||||rs764139323&COSV65068322|4180|1||SNV|HGNC|HGNC:329||||1||||||||1||||||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000466223|retained_intron|3/3||ENST00000466223.1:n.400G>A||400|||||rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|non_coding_transcript_exon_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000478677|retained_intron|2/2||ENST00000478677.1:n.244G>A||244|||||rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron||||||||||rs764139323&COSV65068322|1457|1||SNV|HGNC|HGNC:329||||3||||||||1||||||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron||||||||||rs764139323&COSV65068322|723|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|22/39||ENST00000620552.4:c.3248G>A|ENSP00000484607.1:p.Arg1083Gln|3712|3248|1083|R/Q|cGg/cAg|rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|tolerated(0.39)|benign(0.057)|Gene3D:3.30.70.960&Pfam:PF01390&PROSITE_profiles:PS50024&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00200&Superfamily:SSF82671|||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|21/38||ENST00000651234.1:c.3347G>A|ENSP00000499046.1:p.Arg1116Gln|3797|3347|1116|R/Q|cGg/cAg|rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|tolerated(0.39)|benign(0.292)|Gene3D:3.30.70.960&Pfam:PF01390&PROSITE_profiles:PS50024&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00200&Superfamily:SSF82671|||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||,A|missense_variant|MODERATE|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|21/35||ENST00000652369.1:c.3347G>A|ENSP00000498543.1:p.Arg1116Gln|3797|3347|1116|R/Q|cGg/cAg|rs764139323&COSV65068322||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|tolerated(0.38)|benign(0.292)|Gene3D:3.30.70.960&Pfam:PF01390&PROSITE_profiles:PS50024&PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&SMART:SM00200&Superfamily:SSF82671|||||||||||1.334e-05|0|0|0|5.98e-05|0|2.019e-05|0|0|5.98e-05|gnomAD_EAS|uncertain_significance|0&1|1&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:265,6:0.021:271:109,1:108,3:229,4:131,134,2,4
chr1	1048100	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=102,226|2,6;DP=367;ECNT=2;GERMQ=93;MBQ=37,29;MFRL=120,94;MMQ=60,60;MPOS=27;POPAF=4.61;ROQ=7;TLOD=12.2;CSQ=A|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|23/36||ENST00000379370.7:c.3840G>A|ENSP00000368678.2:p.Pro1280%3D|3893|3840|1280|P|ccG/ccA|rs768974182||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|||PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000461111|retained_intron||||||||||rs768974182|3886|1||SNV|HGNC|HGNC:329||||1||||||||1||||||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000466223|retained_intron||||||||||rs768974182|235|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000478677|retained_intron||||||||||rs768974182|262|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron||||||||||rs768974182|1751|1||SNV|HGNC|HGNC:329||||3||||||||1||||||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron||||||||||rs768974182|429|1||SNV|HGNC|HGNC:329||||2||||||||1||||||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|23/39||ENST00000620552.4:c.3426G>A|ENSP00000484607.1:p.Pro1142%3D|3890|3426|1142|P|ccG/ccA|rs768974182||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|||PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|22/38||ENST00000651234.1:c.3525G>A|ENSP00000499046.1:p.Pro1175%3D|3975|3525|1175|P|ccG/ccA|rs768974182||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|||PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||,A|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|22/35||ENST00000652369.1:c.3525G>A|ENSP00000498543.1:p.Pro1175%3D|3975|3525|1175|P|ccG/ccA|rs768974182||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|||PANTHER:PTHR10913&PANTHER:PTHR10913:SF74&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite|||||||||||0|0|0|0|0|0|0|0|0|0|gnomAD_AFR&gnomAD_AMR&gnomAD_ASJ&gnomAD_EAS&gnomAD_FIN&gnomAD_NFE&gnomAD_OTH&gnomAD_SAS|likely_benign||1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:328,8:0.024:336:79,1:53,1:285,6:102,226,2,6
chr1	1050276	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=158,149|3,4;DP=333;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=121,103;MMQ=60,60;MPOS=23;POPAF=4.31;ROQ=12;TLOD=11.54;CSQ=T|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding|28/36||ENST00000379370.7:c.4923C>T|ENSP00000368678.2:p.Asn1641%3D|4976|4923|1641|N|aaC/aaT|rs148789015||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1|||Gene3D:2.60.120.200&PROSITE_profiles:PS50025&Superfamily:SSF49899&CDD:cd00110|||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|upstream_gene_variant|MODIFIER||ENSG00000242590|Transcript|ENST00000418300|lncRNA||||||||||rs148789015|4757|1||SNV|||YES|||3||||||||||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|upstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000461111|retained_intron||||||||||rs148789015|1710|1||SNV|HGNC|HGNC:329||||1||||||||1||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000466223|retained_intron||||||||||rs148789015|2411|1||SNV|HGNC|HGNC:329||||2||||||||1||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000478677|retained_intron||||||||||rs148789015|2438|1||SNV|HGNC|HGNC:329||||2||||||||1||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000479707|retained_intron||||||||||rs148789015|3927|1||SNV|HGNC|HGNC:329||||3||||||||1||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron||||||||||rs148789015|882|1||SNV|HGNC|HGNC:329||||2||||||||1||||||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding|28/39||ENST00000620552.4:c.4509C>T|ENSP00000484607.1:p.Asn1503%3D|4973|4509|1503|N|aaC/aaT|rs148789015||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1|||Gene3D:2.60.120.200&PROSITE_profiles:PS50025&Superfamily:SSF49899&CDD:cd00110|||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding|27/38||ENST00000651234.1:c.4608C>T|ENSP00000499046.1:p.Asn1536%3D|5058|4608|1536|N|aaC/aaT|rs148789015||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1|||Gene3D:2.60.120.200&PROSITE_profiles:PS50025&Superfamily:SSF49899&CDD:cd00110|||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||,T|synonymous_variant|LOW|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding|27/35||ENST00000652369.1:c.4608C>T|ENSP00000498543.1:p.Asn1536%3D|5058|4608|1536|N|aaC/aaT|rs148789015||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1|||Gene3D:2.60.120.200&PROSITE_profiles:PS50025&Superfamily:SSF49899&CDD:cd00110|||0.0002|0|0|0.001|0|0|||3.203e-05|0|0|0|0.0002752|0|2.662e-05|0|0|0.001|EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:307,7:0.028:314:113,4:120,2:239,6:158,149,3,4
chr1	1054333	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=11,4|3,0;DP=19;ECNT=1;GERMQ=47;MBQ=20,37;MFRL=162,232;MMQ=60,60;MPOS=15;POPAF=7.3;ROQ=17;TLOD=8.79;CSQ=A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000379370|protein_coding||34/35|ENST00000379370.7:c.5877-115G>A|||||||rs538127841&COSV65071368||1||SNV|HGNC|HGNC:329|YES|NM_198576.4||1|P1|CCDS30551.1|ENSP00000368678|O00468.198||UPI00001D7C8B|O00468-6|1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|upstream_gene_variant|MODIFIER||ENSG00000242590|Transcript|ENST00000418300|lncRNA||||||||||rs538127841&COSV65071368|700|1||SNV|||YES|||3||||||||||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000461111|retained_intron||1/2|ENST00000461111.1:n.1993-115G>A|||||||rs538127841&COSV65071368||1||SNV|HGNC|HGNC:329||||1||||||||1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000492947|retained_intron||||||||||rs538127841&COSV65071368|4939|1||SNV|HGNC|HGNC:329||||2||||||||1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000620552|protein_coding||37/38|ENST00000620552.4:c.5532-115G>A|||||||rs538127841&COSV65071368||1||SNV|HGNC|HGNC:329||||5|||ENSP00000484607||A0A087X208.56|UPI0004E4CB7F||1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000651234|protein_coding||36/37|ENST00000651234.1:c.5631-115G>A|||||||rs538127841&COSV65071368||1||SNV|HGNC|HGNC:329|||||||ENSP00000499046||A0A494C1I6.12|UPI000387B6E0||1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||,A|intron_variant|MODIFIER|AGRN|ENSG00000188157|Transcript|ENST00000652369|protein_coding||33/34|ENST00000652369.1:c.5562-115G>A|||||||rs538127841&COSV65071368||1||SNV|HGNC|HGNC:329|||||||ENSP00000498543||A0A494C0G5.12|UPI0010872C9B||1||||||0.0004|0|0|0.002|0|0||||||||||||0.002|EAS||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:15,3:0.251:18:5,2:5,1:11,3:11,4,3,0
chr1	1087520	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=274,114|3,3;DP=420;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=124,91;MMQ=60,60;MPOS=9;POPAF=4.13;ROQ=4;TLOD=8.49;CSQ=T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000379319|protein_coding|5/10||ENST00000379319.5:c.226G>A|ENSP00000368623.1:p.Gly76Ser|533|226|76|G/S|Ggc/Agc|rs750009135||-1||SNV|HGNC|HGNC:26062||||5|P1|CCDS7.2|ENSP00000368623|Q96HA4.131|A0A024R082.57|UPI0000049DAC|Q96HA4-4||tolerated(0.44)|benign(0)|Pfam:PF14946&PANTHER:PTHR16247|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000379320|protein_coding|3/8||ENST00000379320.5:c.226G>A|ENSP00000368624.1:p.Gly76Ser|857|226|76|G/S|Ggc/Agc|rs750009135||-1||SNV|HGNC|HGNC:26062||||2||CCDS85917.1|ENSP00000368624||Q5T2W9.100|UPI0000205ACE|||tolerated(0.64)|benign(0.075)|PANTHER:PTHR16247&Pfam:PF14946|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant&NMD_transcript_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000379325|nonsense_mediated_decay|5/11||ENST00000379325.7:c.226G>A|ENSP00000368629.3:p.Gly76Ser|397|226|76|G/S|Ggc/Agc|rs750009135||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000368629|Q96HA4.131||UPI0000048F44|Q96HA4-3||tolerated(0.44)|benign(0.011)||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000379339|protein_coding|7/12||ENST00000379339.5:c.334G>A|ENSP00000368644.1:p.Gly112Ser|545|334|112|G/S|Ggc/Agc|rs750009135||-1||SNV|HGNC|HGNC:26062||||2||CCDS81250.1|ENSP00000368644|Q96HA4.131||UPI000013EF85|Q96HA4-1||tolerated(0.64)|benign(0.075)|PANTHER:PTHR16247&Pfam:PF14946|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000421241|protein_coding|5/10||ENST00000421241.7:c.226G>A|ENSP00000400736.2:p.Gly76Ser|391|226|76|G/S|Ggc/Agc|rs750009135||-1||SNV|HGNC|HGNC:26062|YES|NM_017891.5||2|P1|CCDS7.2|ENSP00000400736|Q96HA4.131|A0A024R082.57|UPI0000049DAC|Q96HA4-4||tolerated(0.44)|benign(0)|Pfam:PF14946&PANTHER:PTHR16247|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000427787|protein_coding||||||||||rs750009135|2886|-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000395935||B2REC5.57|UPI000173DCFE||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000434641|protein_coding|5/11||ENST00000434641.5:c.226G>A|ENSP00000390635.1:p.Gly76Ser|397|226|76|G/S|Ggc/Agc|rs750009135||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000390635||Q5T2W7.94|UPI0003F47F17|||tolerated(0.51)|benign(0.011)|PANTHER:PTHR16247&Pfam:PF14946|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000442117|protein_coding||||||||||rs750009135|55|-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000416740||B2REC4.67|UPI000173DCFD||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000462097|protein_coding|6/7||ENST00000462097.5:c.226G>A|ENSP00000464273.1:p.Gly76Ser|752|226|76|G/S|Ggc/Agc|rs750009135||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||3|||ENSP00000464273||J3QRL0.37|UPI000268AE20|||tolerated(0.58)|benign(0.011)|Pfam:PF14946&PANTHER:PTHR16247|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|upstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000464905|processed_transcript||||||||||rs750009135|3448|-1||SNV|HGNC|HGNC:26062||||3||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000465822|retained_intron|4/9||ENST00000465822.5:n.335G>A||335|||||rs750009135||-1||SNV|HGNC|HGNC:26062||||2||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant&NMD_transcript_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000467751|nonsense_mediated_decay|6/12||ENST00000467751.5:c.323G>A|ENSP00000463144.1:p.Arg108Gln|488|323|108|R/Q|cGg/cAg|rs750009135||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000463144||J3QKM1.32|UPI0000205ACB||||unknown(0)||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000472741|retained_intron||||||||||rs750009135|3526|-1||SNV|HGNC|HGNC:26062||||4||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000473600|retained_intron|4/5||ENST00000473600.1:n.711G>A||711|||||rs750009135||-1||SNV|HGNC|HGNC:26062||||3||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|C1orf159|ENSG00000131591|Transcript|ENST00000475119|protein_coding|5/6||ENST00000475119.5:c.226G>A|ENSP00000462517.1:p.Gly76Ser|707|226|76|G/S|Ggc/Agc|rs750009135||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||3|||ENSP00000462517||J3KSJ6.37|UPI000268AE21|||tolerated(0.75)|benign(0.011)|Pfam:PF14946&PANTHER:PTHR16247|||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000477196|nonsense_mediated_decay|5/10||ENST00000477196.5:c.*875G>A||1337|||||rs750009135||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000462798||J3KT48.32|UPI000048B028||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000480643|protein_coding||||||||||rs750009135|3980|-1|cds_end_NF|SNV|HGNC|HGNC:26062||||4|||ENSP00000464657||J3QSF0.29|UPI0003F48015||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000482816|processed_transcript|5/10||ENST00000482816.5:n.545G>A||545|||||rs750009135||-1||SNV|HGNC|HGNC:26062||||5||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000487177|retained_intron|1/3||ENST00000487177.5:n.117G>A||117|||||rs750009135||-1||SNV|HGNC|HGNC:26062||||2||||||||||||||||||||||0.0003863|0.0001275|0|0.006043|0|0|0.0001016|0.0002321|0|0.006043|gnomAD_ASJ|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:388,6:0.018:394:145,1:145,2:330,5:274,114,3,3
chr1	1090856	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=131,42|6,2;DP=182;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=122,167;MMQ=60,60;MPOS=8;POPAF=4.61;ROQ=2;TLOD=14.25;CSQ=T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000379319|protein_coding||3/9|ENST00000379319.5:c.73-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||5|P1|CCDS7.2|ENSP00000368623|Q96HA4.131|A0A024R082.57|UPI0000049DAC|Q96HA4-4|||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000379320|protein_coding||1/7|ENST00000379320.5:c.73-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2||CCDS85917.1|ENSP00000368624||Q5T2W9.100|UPI0000205ACE||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000379325|nonsense_mediated_decay||3/10|ENST00000379325.7:c.73-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000368629|Q96HA4.131||UPI0000048F44|Q96HA4-3|||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000379339|protein_coding||5/11|ENST00000379339.5:c.180+20G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2||CCDS81250.1|ENSP00000368644|Q96HA4.131||UPI000013EF85|Q96HA4-1|||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000421241|protein_coding||3/9|ENST00000421241.7:c.73-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062|YES|NM_017891.5||2|P1|CCDS7.2|ENSP00000400736|Q96HA4.131|A0A024R082.57|UPI0000049DAC|Q96HA4-4|||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000427787|protein_coding||4/4|ENST00000427787.5:c.169+422G>A|||||||rs899074232||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000395935||B2REC5.57|UPI000173DCFE||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000434641|protein_coding||3/10|ENST00000434641.5:c.73-428G>A|||||||rs899074232||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000390635||Q5T2W7.94|UPI0003F47F17||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000442117|protein_coding||3/4|ENST00000442117.5:c.73-428G>A|||||||rs899074232||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||5|||ENSP00000416740||B2REC4.67|UPI000173DCFD||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000462097|protein_coding||4/6|ENST00000462097.5:c.73-428G>A|||||||rs899074232||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||3|||ENSP00000464273||J3QRL0.37|UPI000268AE20||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000465822|retained_intron||2/8|ENST00000465822.5:n.182-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2||||||||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000467751|nonsense_mediated_decay||4/11|ENST00000467751.5:c.169+422G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000463144||J3QKM1.32|UPI0000205ACB||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000472741|retained_intron||||||||||rs899074232|190|-1||SNV|HGNC|HGNC:26062||||4||||||||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000473600|retained_intron||2/4|ENST00000473600.1:n.399-269G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||3||||||||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000475119|protein_coding||3/5|ENST00000475119.5:c.73-428G>A|||||||rs899074232||-1|cds_end_NF|SNV|HGNC|HGNC:26062||||3|||ENSP00000462517||J3KSJ6.37|UPI000268AE21||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000477196|nonsense_mediated_decay|4/10||ENST00000477196.5:c.*294G>A||756|||||rs899074232||-1||SNV|HGNC|HGNC:26062||||2|||ENSP00000462798||J3KT48.32|UPI000048B028||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|downstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000480643|protein_coding||||||||||rs899074232|644|-1|cds_end_NF|SNV|HGNC|HGNC:26062||||4|||ENSP00000464657||J3QSF0.29|UPI0003F48015||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000482816|processed_transcript||3/9|ENST00000482816.5:n.392-428G>A|||||||rs899074232||-1||SNV|HGNC|HGNC:26062||||5||||||||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||,T|upstream_gene_variant|MODIFIER|C1orf159|ENSG00000131591|Transcript|ENST00000487177|retained_intron||||||||||rs899074232|3220|-1||SNV|HGNC|HGNC:26062||||2||||||||||||||||||||||1.349e-05|0|0|0|0|0|1.826e-05|0|4.437e-05|4.437e-05|gnomAD_SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:173,8:0.046:181:81,1:63,5:144,6:131,42,6,2
chr1	1127102	.	AC	GT	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,97;MMQ=60,39;MPOS=9;POPAF=7.3;ROQ=7;TLOD=4.2;CSQ=GT|intergenic_variant|MODIFIER|||||||||||||||||||substitution|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,0,1
chr1	1137055	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;GERMQ=31;MBQ=0,37;MFRL=0,134;MMQ=60,60;MPOS=23;POPAF=7.3;ROQ=8;TLOD=3.88;CSQ=A|non_coding_transcript_exon_variant|MODIFIER|LINC01342|ENSG00000223823|Transcript|ENST00000416774|lncRNA|1/3||ENST00000416774.1:n.39G>A||39|||||||1||SNV|HGNC|HGNC:50551|YES|||1|||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344502|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1138185	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;GERMQ=32;MBQ=0,37;MFRL=0,133;MMQ=60,60;MPOS=11;POPAF=7.3;ROQ=7;TLOD=7.88;CSQ=T|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01342|ENSG00000223823|Transcript|ENST00000416774|lncRNA||1/2|ENST00000416774.1:n.94+1075C>T|||||||rs1401909764||1||SNV|HGNC|HGNC:50551|YES|||1|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,2:0.75:2:0,0:0,2:0,2:0,0,2,0
chr1	1179527	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=13,1|2,0;DP=18;ECNT=2;GERMQ=52;MBQ=37,37;MFRL=207,159;MMQ=60,60;MPOS=15;POPAF=7.3;ROQ=15;TLOD=5.1;CSQ=T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379288|protein_coding||||||||||COSV64959712|170|1||SNV|HGNC|HGNC:26693||||1||CCDS8.1|ENSP00000368590|Q6ZVT0.136||UPI000013EF63|Q6ZVT0-3|||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding||4/15|ENST00000379289.6:c.119-130C>T|||||||COSV64959712||1||SNV|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1|||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding||4/15|ENST00000379290.6:c.119-130C>T|||||||COSV64959712||1||SNV|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1|||||||||||||||||||||||||||1|1||||||,T|non_coding_transcript_exon_variant|MODIFIER|TTLL10-AS1|ENSG00000205231|Transcript|ENST00000379317|lncRNA|1/2||ENST00000379317.1:n.29G>A||29|||||COSV64959712||-1||SNV|HGNC|HGNC:41159|YES|||2||||||||||||||||||||||||||||||||||1|1||||||,T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000460998|retained_intron||||||||||COSV64959712|957|1||SNV|HGNC|HGNC:26693||||5||||||||||||||||||||||||||||||||||1|1||||||,T|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000506177|processed_transcript||||||||||COSV64959712|4493|1||SNV|HGNC|HGNC:26693||||4||||||||||||||||||||||||||||||||||1|1||||||,T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000514695|retained_intron||||||||||COSV64959712|1010|1||SNV|HGNC|HGNC:26693||||2||||||||||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000673999|protein_coding||4/5|ENST00000673999.1:c.119-130C>T|||||||COSV64959712||1|cds_end_NF|SNV|HGNC|HGNC:26693|||||||ENSP00000500959||A0A669K9N4.3|UPI001348EF10||||||||||||||||||||||||||||1|1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:14,2:0.174:16:9,1:4,1:13,2:0|1:1179527_C_T:1179527:13,1,2,0
chr1	1179532	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=8,1|6,0;DP=15;ECNT=2;GERMQ=24;MBQ=37,37;MFRL=192,207;MMQ=60,60;MPOS=7;POPAF=7.3;ROQ=28;TLOD=19.21;CSQ=T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379288|protein_coding||||||||||COSV64959869|165|1||SNV|HGNC|HGNC:26693||||1||CCDS8.1|ENSP00000368590|Q6ZVT0.136||UPI000013EF63|Q6ZVT0-3|||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding||4/15|ENST00000379289.6:c.119-125C>T|||||||COSV64959869||1||SNV|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1|||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding||4/15|ENST00000379290.6:c.119-125C>T|||||||COSV64959869||1||SNV|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1|||||||||||||||||||||||||||1|1||||||,T|non_coding_transcript_exon_variant|MODIFIER|TTLL10-AS1|ENSG00000205231|Transcript|ENST00000379317|lncRNA|1/2||ENST00000379317.1:n.24G>A||24|||||COSV64959869||-1||SNV|HGNC|HGNC:41159|YES|||2||||||||||||||||||||||||||||||||||1|1||||||,T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000460998|retained_intron||||||||||COSV64959869|952|1||SNV|HGNC|HGNC:26693||||5||||||||||||||||||||||||||||||||||1|1||||||,T|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000506177|processed_transcript||||||||||COSV64959869|4498|1||SNV|HGNC|HGNC:26693||||4||||||||||||||||||||||||||||||||||1|1||||||,T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000514695|retained_intron||||||||||COSV64959869|1005|1||SNV|HGNC|HGNC:26693||||2||||||||||||||||||||||||||||||||||1|1||||||,T|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000673999|protein_coding||4/5|ENST00000673999.1:c.119-125C>T|||||||COSV64959869||1|cds_end_NF|SNV|HGNC|HGNC:26693|||||||ENSP00000500959||A0A669K9N4.3|UPI001348EF10||||||||||||||||||||||||||||1|1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:9,6:0.437:15:5,4:3,2:8,6:1|0:1179527_C_T:1179527:8,1,6,0
chr1	1180783	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=78,65|2,2;DP=154;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=116,122;MMQ=60,60;MPOS=27;POPAF=7.3;ROQ=5;TLOD=5.73;CSQ=T|synonymous_variant|LOW|TTLL10|ENSG00000162571|Transcript|ENST00000379288|protein_coding|4/9||ENST00000379288.3:c.459C>T|ENSP00000368590.3:p.Ile153%3D|636|459|153|I|atC/atT|rs747645824&COSV101016609||1||SNV|HGNC|HGNC:26693||||1||CCDS8.1|ENSP00000368590|Q6ZVT0.136||UPI000013EF63|Q6ZVT0-3||||PROSITE_profiles:PS51221&PANTHER:PTHR46810|||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|synonymous_variant|LOW|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding|8/16||ENST00000379289.6:c.678C>T|ENSP00000368591.1:p.Ile226%3D|855|678|226|I|atC/atT|rs747645824&COSV101016609||1||SNV|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||PROSITE_profiles:PS51221&PANTHER:PTHR46810|||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|synonymous_variant|LOW|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding|8/16||ENST00000379290.6:c.678C>T|ENSP00000368592.1:p.Ile226%3D|874|678|226|I|atC/atT|rs747645824&COSV101016609||1||SNV|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||PROSITE_profiles:PS51221&PANTHER:PTHR46810|||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|upstream_gene_variant|MODIFIER|TTLL10-AS1|ENSG00000205231|Transcript|ENST00000379317|lncRNA||||||||||rs747645824&COSV101016609|1228|-1||SNV|HGNC|HGNC:41159|YES|||2||||||||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000460998|retained_intron|1/5||ENST00000460998.1:n.300C>T||300|||||rs747645824&COSV101016609||1||SNV|HGNC|HGNC:26693||||5||||||||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000486379|nonsense_mediated_decay||||||||||rs747645824&COSV101016609|4253|1|cds_start_NF|SNV|HGNC|HGNC:26693||||3|||ENSP00000464269||J3QRK8.30|UPI000268AE23||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000514695|retained_intron|2/2||ENST00000514695.1:n.118C>T||118|||||rs747645824&COSV101016609||1||SNV|HGNC|HGNC:26693||||2||||||||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000673999|protein_coding||||||||||rs747645824&COSV101016609|609|1|cds_end_NF|SNV|HGNC|HGNC:26693|||||||ENSP00000500959||A0A669K9N4.3|UPI001348EF10||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918412|TF_binding_site||||||||||rs747645824&COSV101016609||||SNV||||||||||||||||||||||||||||8.416e-06|0|0|0|0|0|0|0|6.965e-05|6.965e-05|gnomAD_SAS||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:143,4:0.033:147:41,2:64,1:114,3:78,65,2,2
chr1	1182517	.	CT	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=10,68|1,3;DP=84;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=159,135;MMQ=60,60;MPOS=27;POPAF=7.3;ROQ=93;TLOD=5.55;CSQ=-|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379288|protein_coding||6/8|ENST00000379288.3:c.697+72del|||||||||1||deletion|HGNC|HGNC:26693||||1||CCDS8.1|ENSP00000368590|Q6ZVT0.136||UPI000013EF63|Q6ZVT0-3||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding||10/15|ENST00000379289.6:c.916+72del|||||||||1||deletion|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding||10/15|ENST00000379290.6:c.916+72del|||||||||1||deletion|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|TTLL10-AS1|ENSG00000205231|Transcript|ENST00000379317|lncRNA|||||||||||2963|-1||deletion|HGNC|HGNC:41159|YES|||2|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000460998|retained_intron||3/4|ENST00000460998.1:n.538+72del|||||||||1||deletion|HGNC|HGNC:26693||||5|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000486379|nonsense_mediated_decay|||||||||||2518|1|cds_start_NF|deletion|HGNC|HGNC:26693||||3|||ENSP00000464269||J3QRK8.30|UPI000268AE23|||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000514695|retained_intron|||||||||||1634|1||deletion|HGNC|HGNC:26693||||2|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000673999|protein_coding|||||||||||2344|1|cds_end_NF|deletion|HGNC|HGNC:26693|||||||ENSP00000500959||A0A669K9N4.3|UPI001348EF10|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:78,4:0.054:82:20,1:22,0:68,3:10,68,1,3
chr1	1185203	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=5,57|0,3;DP=65;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=136,144;MMQ=60,60;MPOS=25;POPAF=4.31;ROQ=8;TLOD=6.21;CSQ=A|3_prime_UTR_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379288|protein_coding|9/9||ENST00000379288.3:c.*61G>A||1453|||||rs368596048||1||SNV|HGNC|HGNC:26693||||1||CCDS8.1|ENSP00000368590|Q6ZVT0.136||UPI000013EF63|Q6ZVT0-3||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding||13/15|ENST00000379289.6:c.1401+94G>A|||||||rs368596048||1||SNV|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding||13/15|ENST00000379290.6:c.1401+94G>A|||||||rs368596048||1||SNV|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000460998|retained_intron||||||||||rs368596048|1276|1||SNV|HGNC|HGNC:26693||||5|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000486379|nonsense_mediated_decay||1/4|ENST00000486379.1:c.74+94G>A|||||||rs368596048||1|cds_start_NF|SNV|HGNC|HGNC:26693||||3|||ENSP00000464269||J3QRK8.30|UPI000268AE23|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000514695|retained_intron||||||||||rs368596048|4319|1||SNV|HGNC|HGNC:26693||||2|||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164822|enhancer||||||||||rs368596048||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000166069|||||||||||rs368596048||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0086|13|N|0.004|EGR1&EGR2&EGR4&EGR3	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:62,3:0.064:65:22,1:35,2:57,3:5,57,0,3
chr1	1196891	.	A	AGGGGG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=1,5|0,2;DP=9;ECNT=1;GERMQ=12;MBQ=37,29;MFRL=261,210;MMQ=60,60;MPOS=7;POPAF=7.3;ROQ=93;TLOD=6.58;CSQ=GGGGG|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379289|protein_coding||14/15|ENST00000379289.6:c.1518+175_1518+176insGGGGG|||||||||1||insertion|HGNC|HGNC:26693|YES|NM_001130045.2||2|P1|CCDS44036.1|ENSP00000368591|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,GGGGG|intron_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000379290|protein_coding||14/15|ENST00000379290.6:c.1518+175_1518+176insGGGGG|||||||||1||insertion|HGNC|HGNC:26693||||1|P1|CCDS44036.1|ENSP00000368592|Q6ZVT0.136||UPI0000205ADB|Q6ZVT0-1||||||||||||||||||||||||||||||||||,GGGGG|intron_variant&NMD_transcript_variant|MODIFIER|TTLL10|ENSG00000162571|Transcript|ENST00000486379|nonsense_mediated_decay||3/4|ENST00000486379.1:c.*157+175_*157+176insGGGGG|||||||||1|cds_start_NF|insertion|HGNC|HGNC:26693||||3|||ENSP00000464269||J3QRK8.30|UPI000268AE23|||||||||||||||||||||||||||||||||||,GGGGG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344529|CTCF_binding_site||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:6,2:0.3:8:1,1:5,1:6,2:1,5,0,2
chr1	1204533	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=10,34|0,3;DP=47;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=130,134;MMQ=60,60;MPOS=17;POPAF=7.3;ROQ=3;TLOD=5.65;CSQ=A|intron_variant|MODIFIER|TNFRSF18|ENSG00000186891|Transcript|ENST00000328596|protein_coding||2/3|ENST00000328596.10:c.311-47C>T|||||||rs1052111904||-1||SNV|HGNC|HGNC:11914||||1||CCDS9.1|ENSP00000328207|Q9Y5U5.175||UPI000002B5CE|Q9Y5U5-2||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|TNFRSF18|ENSG00000186891|Transcript|ENST00000379265|protein_coding||2/4|ENST00000379265.5:c.311-47C>T|||||||rs1052111904||-1||SNV|HGNC|HGNC:11914||||1|A2|CCDS30552.1|ENSP00000368567|Q9Y5U5.175||UPI000015B651|Q9Y5U5-3||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|TNFRSF18|ENSG00000186891|Transcript|ENST00000379268|protein_coding||2/4|ENST00000379268.7:c.311-47C>T|||||||rs1052111904||-1||SNV|HGNC|HGNC:11914|YES|NM_004195.3||1|P4|CCDS10.1|ENSP00000368570|Q9Y5U5.175||UPI0000035975|Q9Y5U5-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|TNFRSF18|ENSG00000186891|Transcript|ENST00000486728|protein_coding||1/3|ENST00000486728.5:c.95-47C>T|||||||rs1052111904||-1||SNV|HGNC|HGNC:11914||||1|A2||ENSP00000462735||J3KT02.55|UPI000268AE24|||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344533|promoter||||||||||rs1052111904||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:44,3:0.08:47:7,0:4,0:44,3:10,34,0,3
chr1	1205436	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=169,130|2,1;DP=320;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=129,132;MMQ=60,60;MPOS=43;POPAF=7.3;ROQ=5;TLOD=6.51;CSQ=T|missense_variant|MODERATE|TNFRSF18|ENSG00000186891|Transcript|ENST00000328596|protein_coding|2/4||ENST00000328596.10:c.244G>A|ENSP00000328207.6:p.Gly82Arg|244|244|82|G/R|Gga/Aga|rs1271110528&COSV100148848&COSV100148938||-1||SNV|HGNC|HGNC:11914||||1||CCDS9.1|ENSP00000328207|Q9Y5U5.175||UPI000002B5CE|Q9Y5U5-2||tolerated_low_confidence(0.28)|benign(0.046)|CDD:cd13417&PANTHER:PTHR47388&Gene3D:2.10.50.10|||||||||||8.029e-06|0|0|0|0|0|1.785e-05|0|0|1.785e-05|gnomAD_NFE||0&1&1|0&1&1||||||,T|missense_variant|MODERATE|TNFRSF18|ENSG00000186891|Transcript|ENST00000379265|protein_coding|2/5||ENST00000379265.5:c.244G>A|ENSP00000368567.5:p.Gly82Arg|244|244|82|G/R|Gga/Aga|rs1271110528&COSV100148848&COSV100148938||-1||SNV|HGNC|HGNC:11914||||1|A2|CCDS30552.1|ENSP00000368567|Q9Y5U5.175||UPI000015B651|Q9Y5U5-3||tolerated(0.5)|benign(0.04)|Gene3D:2.10.50.10&PANTHER:PTHR47388&CDD:cd13417|||||||||||8.029e-06|0|0|0|0|0|1.785e-05|0|0|1.785e-05|gnomAD_NFE||0&1&1|0&1&1||||||,T|missense_variant|MODERATE|TNFRSF18|ENSG00000186891|Transcript|ENST00000379268|protein_coding|2/5||ENST00000379268.7:c.244G>A|ENSP00000368570.2:p.Gly82Arg|265|244|82|G/R|Gga/Aga|rs1271110528&COSV100148848&COSV100148938||-1||SNV|HGNC|HGNC:11914|YES|NM_004195.3||1|P4|CCDS10.1|ENSP00000368570|Q9Y5U5.175||UPI0000035975|Q9Y5U5-1||tolerated(0.3)|benign(0.04)|PDB-ENSP_mappings:7khd.C&PDB-ENSP_mappings:7khd.D&CDD:cd13417&PANTHER:PTHR47388&Gene3D:2.10.50.10|||||||||||8.029e-06|0|0|0|0|0|1.785e-05|0|0|1.785e-05|gnomAD_NFE||0&1&1|0&1&1||||||,T|missense_variant|MODERATE|TNFRSF18|ENSG00000186891|Transcript|ENST00000486728|protein_coding|1/4||ENST00000486728.5:c.28G>A|ENSP00000462735.1:p.Gly10Arg|245|28|10|G/R|Gga/Aga|rs1271110528&COSV100148848&COSV100148938||-1||SNV|HGNC|HGNC:11914||||1|A2||ENSP00000462735||J3KT02.55|UPI000268AE24|||tolerated(0.21)|benign(0.04)|CDD:cd13417&PANTHER:PTHR47388&Gene3D:2.10.50.10|||||||||||8.029e-06|0|0|0|0|0|1.785e-05|0|0|1.785e-05|gnomAD_NFE||0&1&1|0&1&1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344533|promoter||||||||||rs1271110528&COSV100148848&COSV100148938||||SNV||||||||||||||||||||||||||||8.029e-06|0|0|0|0|0|1.785e-05|0|0|1.785e-05|gnomAD_NFE||0&1&1|0&1&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:299,3:0.011:302:111,1:109,1:266,2:0|1:1205419_C_T:1205419:169,130,2,1
chr1	1212158	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=15,83|1,5;DP=105;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=139,152;MMQ=60,60;MPOS=23;POPAF=7.3;ROQ=8;TLOD=13.09;CSQ=A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding||||||||||rs748910098|4773|-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding||||||||||rs748910098|4773|-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|intron_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000379236|protein_coding||4/6|ENST00000379236.4:c.438-20C>T|||||||rs748910098||-1||SNV|HGNC|HGNC:11918|YES|NM_003327.4||1|P1|CCDS11.1|ENSP00000368538|P43489.177||UPI00001370E5||1||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000453580|processed_transcript||3/3|ENST00000453580.1:n.274-20C>T|||||||rs748910098||-1||SNV|HGNC|HGNC:11918||||3||||||||1||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay||||||||||rs748910098|4773|-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron||||||||||rs748910098|4776|-1||SNV|HGNC|HGNC:24188||||2||||||||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron||||||||||rs748910098|4774|-1||SNV|HGNC|HGNC:24188||||2||||||||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000497869|retained_intron||3/4|ENST00000497869.5:n.1018-20C>T|||||||rs748910098||-1||SNV|HGNC|HGNC:11918||||2||||||||1||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding||||||||||rs748910098|4751|-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6|||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344538|promoter||||||||||rs748910098||||SNV||||||||||||||||||||||||||||2.036e-05|6.414e-05|0.0001166|0|0|0|0|0|0|0.0001166|gnomAD_AMR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:98,6:0.076:104:36,1:44,5:84,6:0|1:1212158_G_A:1212158:15,83,1,5
chr1	1212180	.	T	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=3,60|0,2;DP=66;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=141,146;MMQ=60,60;MPOS=24;POPAF=7.3;ROQ=2;TLOD=3.25;CSQ=C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding||||||||||rs773663465|4751|-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding||||||||||rs773663465|4751|-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|intron_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000379236|protein_coding||4/6|ENST00000379236.4:c.438-42A>G|||||||rs773663465||-1||SNV|HGNC|HGNC:11918|YES|NM_003327.4||1|P1|CCDS11.1|ENSP00000368538|P43489.177||UPI00001370E5||1||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000453580|processed_transcript||3/3|ENST00000453580.1:n.274-42A>G|||||||rs773663465||-1||SNV|HGNC|HGNC:11918||||3||||||||1||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay||||||||||rs773663465|4751|-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron||||||||||rs773663465|4754|-1||SNV|HGNC|HGNC:24188||||2||||||||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron||||||||||rs773663465|4752|-1||SNV|HGNC|HGNC:24188||||2||||||||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000497869|retained_intron||3/4|ENST00000497869.5:n.1018-42A>G|||||||rs773663465||-1||SNV|HGNC|HGNC:11918||||2||||||||1||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding||||||||||rs773663465|4729|-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6|||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||,C|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344538|promoter||||||||||rs773663465||||SNV||||||||||||||||||||||||||||4.225e-05|0|0|0|0.0005673|0|0|0|0|0.0005673|gnomAD_EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:63,2:0.046:65:16,0:39,2:60,2:1|0:1212158_G_A:1212158:3,60,0,2
chr1	1212957	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=145,26|2,2;DP=190;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=139,260;MMQ=60,60;MPOS=79;POPAF=7.3;ROQ=9;TLOD=3.59;CSQ=T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|||||||||||3974|-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|||||||||||3974|-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000379236|protein_coding||3/6|ENST00000379236.4:c.370+35G>A|||||||||-1||SNV|HGNC|HGNC:11918|YES|NM_003327.4||1|P1|CCDS11.1|ENSP00000368538|P43489.177||UPI00001370E5||1|||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000453580|processed_transcript||2/3|ENST00000453580.1:n.206+35G>A|||||||||-1||SNV|HGNC|HGNC:11918||||3||||||||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|||||||||||3974|-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron|||||||||||3977|-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron|||||||||||3975|-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000497869|retained_intron||2/4|ENST00000497869.5:n.950+35G>A|||||||||-1||SNV|HGNC|HGNC:11918||||2||||||||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|||||||||||3952|-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344538|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:171,4:0.019:175:79,1:69,1:152,2:145,26,2,2
chr1	1217308	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=2;GERMQ=31;MBQ=0,37;MFRL=0,192;MMQ=60,60;MPOS=20;POPAF=7.3;ROQ=6;TLOD=3.88;CSQ=A|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|7/7||ENST00000263741.12:c.*362C>T||1702|||||rs1157690465||-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|7/7||ENST00000360001.12:c.*204C>T||1556|||||rs1157690465||-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000379236|protein_coding||||||||||rs1157690465|3155|-1||SNV|HGNC|HGNC:11918|YES|NM_003327.4||1|P1|CCDS11.1|ENSP00000368538|P43489.177||UPI00001370E5||1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding||||||||||rs1157690465|1215|-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000453580|processed_transcript||||||||||rs1157690465|3810|-1||SNV|HGNC|HGNC:11918||||3||||||||1|||||||||||||||||||||||||||||||||,A|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|7/7||ENST00000465727.5:c.*660C>T||1718|||||rs1157690465||-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron|2/2||ENST00000478938.1:n.2217C>T||2217|||||rs1157690465||-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron|3/3||ENST00000494748.1:n.3140C>T||3140|||||rs1157690465||-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000497869|retained_intron||||||||||rs1157690465|3170|-1||SNV|HGNC|HGNC:11918||||2||||||||1|||||||||||||||||||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|7/7||ENST00000660930.1:c.*362C>T||1738|||||rs1157690465||-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344538|promoter||||||||||rs1157690465||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,1:0,0:0,1:0,0,1,0
chr1	1217431	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=38,7|3,1;DP=58;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=152,123;MMQ=60,60;MPOS=7;POPAF=7.3;ROQ=11;TLOD=7.54;CSQ=T|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|7/7||ENST00000263741.12:c.*239G>A||1579|||||||-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|7/7||ENST00000360001.12:c.*81G>A||1433|||||||-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000379236|protein_coding|||||||||||3278|-1||SNV|HGNC|HGNC:11918|YES|NM_003327.4||1|P1|CCDS11.1|ENSP00000368538|P43489.177||UPI00001370E5||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding|||||||||||1092|-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000453580|processed_transcript|||||||||||3933|-1||SNV|HGNC|HGNC:11918||||3||||||||1|||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|7/7||ENST00000465727.5:c.*537G>A||1595|||||||-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron|2/2||ENST00000478938.1:n.2094G>A||2094|||||||-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron|3/3||ENST00000494748.1:n.3017G>A||3017|||||||-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|TNFRSF4|ENSG00000186827|Transcript|ENST00000497869|retained_intron|||||||||||3293|-1||SNV|HGNC|HGNC:11918||||2||||||||1|||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|7/7||ENST00000660930.1:c.*239G>A||1615|||||||-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344538|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:45,4:0.089:49:21,1:18,2:39,3:38,7,3,1
chr1	1223443	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=1,2|0,2;DP=5;ECNT=1;GERMQ=27;MBQ=37,37;MFRL=159,225;MMQ=60,60;MPOS=3;POPAF=7.3;ROQ=8;TLOD=6.58;CSQ=A|intron_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding||3/6|ENST00000263741.12:c.443-86G>T|||||||||-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding||3/6|ENST00000360001.12:c.443-86G>T|||||||||-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding||2/4|ENST00000403997.2:c.267-86G>T|||||||||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|||||||||||3829|-1||SNV|HGNC|HGNC:24188||||5|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay||3/6|ENST00000465727.5:c.464-86G>T|||||||||-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron|||||||||||3150|-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron|||||||||||2092|-1||SNV|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding||3/6|ENST00000660930.1:c.464-86G>T|||||||||-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:3,2:0.429:5:2,2:1,0:3,2:1,2,0,2
chr1	1223969	.	C	CCCATTTGCTGTCTTGCAGGG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=21,83|0,4;DP=118;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=129,83;MMQ=60,60;MPOS=22;POPAF=7.3;ROQ=93;TLOD=9.08;CSQ=CCATTTGCTGTCTTGCAGGG|splice_acceptor_variant|HIGH|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding||2/6|ENST00000263741.12:c.306-2_306-1insCCCTGCAAGACAGCAAATGG|||||||||-1||insertion|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|splice_acceptor_variant|HIGH|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding||2/6|ENST00000360001.12:c.306-2_306-1insCCCTGCAAGACAGCAAATGG|||||||||-1||insertion|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|splice_acceptor_variant|HIGH|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding||1/4|ENST00000403997.2:c.130-2_130-1insCCCTGCAAGACAGCAAATGG|||||||||-1|cds_start_NF&cds_end_NF|insertion|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|downstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|||||||||||3302|-1||insertion|HGNC|HGNC:24188||||5|||||||||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|splice_acceptor_variant&NMD_transcript_variant|HIGH|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay||2/6|ENST00000465727.5:c.327-2_327-1insCCCTGCAAGACAGCAAATGG|||||||||-1||insertion|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000478938|retained_intron|||||||||||3676|-1||insertion|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000494748|retained_intron|||||||||||2618|-1||insertion|HGNC|HGNC:24188||||2|||||||||||||||||||||||||||||||||||||||||,CCATTTGCTGTCTTGCAGGG|splice_acceptor_variant|HIGH|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding||2/6|ENST00000660930.1:c.327-2_327-1insCCCTGCAAGACAGCAAATGG|||||||||-1||insertion|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:104,4:0.047:108:21,0:29,1:128,4:0|1:1223968_C_CTG:1223968:21,83,0,4
chr1	1228504	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=177,112|8,2;DP=322;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=137,163;MMQ=60,60;MPOS=26;POPAF=4.31;ROQ=9;TLOD=18.45;CSQ=T|missense_variant|MODERATE|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|2/7||ENST00000263741.12:c.269G>A|ENSP00000263741.8:p.Arg90Gln|583|269|90|R/Q|cGg/cAg|rs369730325||-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||tolerated(0.1)|possibly_damaging(0.454)|Gene3D:1.10.238.10&PANTHER:PTHR10827&PANTHER:PTHR10827:SF51&CDD:cd16225|||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|2/7||ENST00000360001.12:c.269G>A|ENSP00000353094.7:p.Arg90Gln|553|269|90|R/Q|cGg/cAg|rs369730325||-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||tolerated(0.11)|benign(0.084)|PANTHER:PTHR10827&PANTHER:PTHR10827:SF51&Superfamily:SSF47473&CDD:cd16225|||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|upstream_gene_variant|MODIFIER|B3GALT6|ENSG00000176022|Transcript|ENST00000379198|protein_coding||||||||||rs369730325|3733|1||SNV|HGNC|HGNC:17978|YES|NM_080605.4|||P1|CCDS13.1|ENSP00000368496|Q96L58.159||UPI0000141885||1||||||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding|1/5||ENST00000403997.2:c.95G>A|ENSP00000384207.2:p.Arg32Gln|93|95|32|R/Q|cGg/cAg|rs369730325||-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||tolerated(0.1)|benign(0.04)|PANTHER:PTHR10827&PANTHER:PTHR10827:SF51&CDD:cd16225|||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|2/3||ENST00000459994.2:n.520G>A||520|||||rs369730325||-1||SNV|HGNC|HGNC:24188||||5||||||||||||||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|missense_variant&NMD_transcript_variant|MODERATE|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|2/7||ENST00000465727.5:c.290G>A|ENSP00000435962.1:p.Arg97Gln|583|290|97|R/Q|cGg/cAg|rs369730325||-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||tolerated(0.13)|possibly_damaging(0.663)||||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||,T|missense_variant|MODERATE|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|2/7||ENST00000660930.1:c.290G>A|ENSP00000499296.1:p.Arg97Gln|619|290|97|R/Q|cGg/cAg|rs369730325||-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||tolerated(0.1)|possibly_damaging(0.454)|PANTHER:PTHR10827&PANTHER:PTHR10827:SF51&CDD:cd16225|||||||||0|0.0002326|0.0001248|0|0|0.001419|0|4.637e-05|5.376e-05|0|0.0003274|0.001419|gnomAD_ASJ|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:289,10:0.039:299:70,6:112,2:242,9:177,112,8,2
chr1	1231926	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;GERMQ=32;MBQ=0,20;MFRL=0,102;MMQ=60,60;MPOS=15;POPAF=7.3;ROQ=5;TLOD=4.62;CSQ=A|5_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|1/7||ENST00000263741.12:c.-209C>T||106|||||||-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,A|5_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|1/7||ENST00000360001.12:c.-209C>T||76|||||||-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|B3GALT6|ENSG00000176022|Transcript|ENST00000379198|protein_coding|||||||||||311|1||SNV|HGNC|HGNC:17978|YES|NM_080605.4|||P1|CCDS13.1|ENSP00000368496|Q96L58.159||UPI0000141885||1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding|||||||||||3330|-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|1/3||ENST00000459994.2:n.43C>T||43|||||||-1||SNV|HGNC|HGNC:24188||||5|||||||||||||||||||||||||||||||||||||||||,A|5_prime_UTR_variant&NMD_transcript_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|1/7||ENST00000465727.5:c.-188C>T||106|||||||-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,A|5_prime_UTR_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|1/7||ENST00000660930.1:c.-188C>T||142|||||||-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000159|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00205869459|||||||||||||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0104|4|Y|-0.059|ETV2::PAX5&ELK1::PAX1&ELK1::PAX5&ELK1::PAX9,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00205756653|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0092|23|N|-0.066|ELK1::TBX21&ERF::EOMES&ERF::TBX21	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,2:0.667:2:0,0:0,1:0,1:0,0,1,1
chr1	1233361	.	C	CG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=4,14|0,3;DP=23;ECNT=2;GERMQ=36;MBQ=37,37;MFRL=198,129;MMQ=60,60;MPOS=5;POPAF=7.3;ROQ=93;TLOD=9.38;CSQ=G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|||||||||||1330|-1||insertion|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|||||||||||1360|-1||insertion|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,G|3_prime_UTR_variant|MODIFIER|B3GALT6|ENSG00000176022|Transcript|ENST00000379198|protein_coding|1/1||ENST00000379198.5:c.*93_*94insG||1125-1126|||||||1||insertion|HGNC|HGNC:17978|YES|NM_080605.4|||P1|CCDS13.1|ENSP00000368496|Q96L58.159||UPI0000141885||1|||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding|||||||||||4765|-1|cds_start_NF&cds_end_NF|insertion|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|||||||||||1393|-1||insertion|HGNC|HGNC:24188||||5|||||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|||||||||||1330|-1||insertion|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|||||||||||1294|-1||insertion|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000159|promoter||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:18,3:0.208:21:5,2:6,1:14,3:0|1:1233361_C_CG:1233361:4,14,0,3
chr1	1233364	.	C	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=4,14|0,3;DP=21;ECNT=2;GERMQ=55;MBQ=37,37;MFRL=198,129;MMQ=60,60;MPOS=1;POPAF=7.3;ROQ=40;TLOD=9.4;CSQ=G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000263741|protein_coding|||||||||||1333|-1||SNV|HGNC|HGNC:24188||||1|A2||ENSP00000263741||A0A5F9UJX7.7|UPI00114AF40C|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000360001|protein_coding|||||||||||1363|-1||SNV|HGNC|HGNC:24188|YES|NM_016176.6||1|P2||ENSP00000353094||A0A5F9UP49.7|UPI0000205990|||||||||||||||||||||||||||||||||||,G|3_prime_UTR_variant|MODIFIER|B3GALT6|ENSG00000176022|Transcript|ENST00000379198|protein_coding|1/1||ENST00000379198.5:c.*96C>G||1128|||||||1||SNV|HGNC|HGNC:17978|YES|NM_080605.4|||P1|CCDS13.1|ENSP00000368496|Q96L58.159||UPI0000141885||1|||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000403997|protein_coding|||||||||||4768|-1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:24188||||3|||ENSP00000384207||H0Y3T6.56|UPI000059CF48|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000459994|processed_transcript|||||||||||1396|-1||SNV|HGNC|HGNC:24188||||5|||||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000465727|nonsense_mediated_decay|||||||||||1333|-1||SNV|HGNC|HGNC:24188||||2|||ENSP00000435962||G3V1E2.92|UPI000045610D|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|SDF4|ENSG00000078808|Transcript|ENST00000660930|protein_coding|||||||||||1297|-1||SNV|HGNC|HGNC:24188|||||A2|CCDS12.1|ENSP00000499296|Q9BRK5.187|A0A024R0A9.40|UPI000013D454|Q9BRK5-6||||||||||||||||||||||||||||||||||,G|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000159|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:18,3:0.21:21:4,2:2,1:14,3:0|1:1233361_C_CG:1233361:4,14,0,3
chr1	1242769	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=50,16|21,10;DP=109;ECNT=1;GERMQ=10;MBQ=37,37;MFRL=147,151;MMQ=60,60;MPOS=14;POPAF=3.53;ROQ=84;TLOD=88.54;CSQ=T|intron_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding||7/7|ENST00000330388.2:c.810+66G>A|||||||rs541437611||-1||SNV|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A||||||||0.0012|0|0|0|0|0.0061||||||||||||0.0061|SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron||2/2|ENST00000462849.1:n.481+66G>A|||||||rs541437611||-1||SNV|HGNC|HGNC:32308||||2||||||||||||||0.0012|0|0|0|0|0.0061||||||||||||0.0061|SAS|||||||||,T|downstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron||||||||||rs541437611|497|-1||SNV|HGNC|HGNC:32308||||3||||||||||||||0.0012|0|0|0|0|0.0061||||||||||||0.0061|SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron||1/1|ENST00000478606.1:n.324+66G>A|||||||rs541437611||-1||SNV|HGNC|HGNC:32308||||2||||||||||||||0.0012|0|0|0|0|0.0061||||||||||||0.0061|SAS|||||||||,T|downstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron||||||||||rs541437611|1212|-1||SNV|HGNC|HGNC:32308||||3||||||||||||||0.0012|0|0|0|0|0.0061||||||||||||0.0061|SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:66,31:0.328:97:32,11:23,15:56,27:50,16,21,10
chr1	1243520	.	G	GGTGCCTTCCTGC	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=91,176|2,2;DP=309;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=117,116;MMQ=60,60;MPOS=26;POPAF=7.3;ROQ=93;TLOD=7.75;CSQ=GTGCCTTCCTGC|inframe_insertion|MODERATE|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding|5/8||ENST00000330388.2:c.563_564insGCAGGAAGGCAC|ENSP00000329137.2:p.Ser188_Gly189insGlnGluGlyThr|595-596|563-564|188|S/SQEGT|tcc/tcGCAGGAAGGCACc|||-1||insertion|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A|||||Gene3D:2.60.120.40&PROSITE_profiles:PS50871&PANTHER:PTHR24019&PANTHER:PTHR24019:SF12&Superfamily:SSF49842||||||||||||||||||||||||||||||,GTGCCTTCCTGC|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron|||||||||||57|-1||insertion|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,GTGCCTTCCTGC|non_coding_transcript_exon_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron|3/3||ENST00000468365.1:n.392_393insGCAGGAAGGCAC||392-393|||||||-1||insertion|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||,GTGCCTTCCTGC|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron|||||||||||362|-1||insertion|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,GTGCCTTCCTGC|downstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron|||||||||||460|-1||insertion|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:267,4:0.021:271:68,1:44,1:255,4:0|1:1243520_G_GGTGCCTTCCTGC:1243520:91,176,2,2
chr1	1243522	.	A	AGGCTCCGGTCTGAGCCTG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=91,182|2,2;DP=297;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=117,116;MMQ=60,60;MPOS=8;POPAF=7.3;ROQ=93;TLOD=7.59;CSQ=GGCTCCGGTCTGAGCCTG|inframe_insertion|MODERATE|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding|5/8||ENST00000330388.2:c.561_562insCAGGCTCAGACCGGAGCC|ENSP00000329137.2:p.Gly187_Ser188insGlnAlaGlnThrGlyAla|593-594|561-562|187-188|-/QAQTGA|-/CAGGCTCAGACCGGAGCC|||-1||insertion|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A|||||Gene3D:2.60.120.40&PROSITE_profiles:PS50871&PANTHER:PTHR24019&PANTHER:PTHR24019:SF12&Superfamily:SSF49842||||||||||||||||||||||||||||||,GGCTCCGGTCTGAGCCTG|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron|||||||||||59|-1||insertion|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,GGCTCCGGTCTGAGCCTG|non_coding_transcript_exon_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron|3/3||ENST00000468365.1:n.390_391insCAGGCTCAGACCGGAGCC||390-391|||||||-1||insertion|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||,GGCTCCGGTCTGAGCCTG|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron|||||||||||364|-1||insertion|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,GGCTCCGGTCTGAGCCTG|downstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron|||||||||||458|-1||insertion|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:273,4:0.02:277:68,1:46,3:257,4:0|1:1243520_G_GGTGCCTTCCTGC:1243520:91,182,2,2
chr1	1243665	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,6|0,4;DP=10;ECNT=2;GERMQ=25;MBQ=37,37;MFRL=203,216;MMQ=60,60;MPOS=18;POPAF=7.3;ROQ=34;TLOD=12.14;CSQ=A|intron_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding||4/7|ENST00000330388.2:c.532-113C>T|||||||||-1||SNV|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron|||||||||||202|-1||SNV|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron||2/2|ENST00000468365.1:n.361-113C>T|||||||||-1||SNV|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron|||||||||||507|-1||SNV|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron|||||||||||316|-1||SNV|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:6,4:0.417:10:3,2:3,2:6,4:0,6,0,4
chr1	1243997	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=145,94|4,2;DP=256;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=127,155;MMQ=60,60;MPOS=10;POPAF=4.01;ROQ=16;TLOD=7.91;CSQ=T|missense_variant|MODERATE|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding|4/8||ENST00000330388.2:c.488G>A|ENSP00000329137.2:p.Arg163Gln|520|488|163|R/Q|cGg/cAg|rs755988091||-1||SNV|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A|||tolerated(0.65)|benign(0)|PROSITE_profiles:PS50871&PANTHER:PTHR24019&PANTHER:PTHR24019:SF12&Superfamily:SSF49842|||||||||||0.0001116|0.0002369|0.0001806|0|0|0.0004138|1.026e-05|0.0007294|0.000102|0.0007294|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron||||||||||rs755988091|534|-1||SNV|HGNC|HGNC:32308||||2||||||||||||||||||||||0.0001116|0.0002369|0.0001806|0|0|0.0004138|1.026e-05|0.0007294|0.000102|0.0007294|gnomAD_OTH|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron|2/3||ENST00000468365.1:n.317G>A||317|||||rs755988091||-1||SNV|HGNC|HGNC:32308||||3||||||||||||||||||||||0.0001116|0.0002369|0.0001806|0|0|0.0004138|1.026e-05|0.0007294|0.000102|0.0007294|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron||||||||||rs755988091|839|-1||SNV|HGNC|HGNC:32308||||2||||||||||||||||||||||0.0001116|0.0002369|0.0001806|0|0|0.0004138|1.026e-05|0.0007294|0.000102|0.0007294|gnomAD_OTH|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron|2/2||ENST00000486627.1:n.623G>A||623|||||rs755988091||-1||SNV|HGNC|HGNC:32308||||3||||||||||||||||||||||0.0001116|0.0002369|0.0001806|0|0|0.0004138|1.026e-05|0.0007294|0.000102|0.0007294|gnomAD_OTH|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:239,6:0.023:245:81,2:110,2:207,4:145,94,4,2
chr1	1246138	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,115;MMQ=60,60;MPOS=18;POPAF=7.3;ROQ=10;TLOD=3.88;CSQ=T|intron_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000330388|protein_coding||1/7|ENST00000330388.2:c.177+376G>A|||||||||-1||SNV|HGNC|HGNC:32308|YES|NM_001014980.3||1|P1|CCDS30554.1|ENSP00000329137|Q5T7M4.106||UPI00001D7E7A|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000462849|retained_intron|||||||||||2675|-1||SNV|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000468365|retained_intron|||||||||||1720|-1||SNV|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000478606|retained_intron|||||||||||2980|-1||SNV|HGNC|HGNC:32308||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|C1QTNF12|ENSG00000184163|Transcript|ENST00000486627|retained_intron|||||||||||1414|-1||SNV|HGNC|HGNC:32308||||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER||ENSG00000260179|Transcript|ENST00000565563|lncRNA|||||||||||3639|-1||SNV|||YES||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1257001	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=107,41|4,1;DP=166;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=128,142;MMQ=60,60;MPOS=20;POPAF=7.3;ROQ=18;TLOD=8.26;CSQ=T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000347370|protein_coding|5/7||ENST00000347370.6:c.249G>A|ENSP00000344857.2:p.Ser83%3D|723|249|83|S|tcG/tcA|rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000344857||A6NGS0.123|UPI00001D69FA|||||Gene3D:3.10.110.10&PROSITE_profiles:PS50127&PANTHER:PTHR24068&PANTHER:PTHR24068:SF135&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000349431|protein_coding|5/7||ENST00000349431.11:c.405G>A|ENSP00000305826.7:p.Ser135%3D|594|405|135|S|tcG/tcA|rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268|YES|NM_058167.3||1|P1|CCDS14.1|ENSP00000305826|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||PDB-ENSP_mappings:2f4w.A&PDB-ENSP_mappings:2f4w.B&PROSITE_profiles:PS50127&PANTHER:PTHR24067&PANTHER:PTHR24067:SF257&Gene3D:3.10.110.10&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000360466|protein_coding|5/7||ENST00000360466.6:c.405G>A|ENSP00000353653.2:p.Ser135%3D|633|405|135|S|tcG/tcA|rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||2|P1|CCDS14.1|ENSP00000353653|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||PDB-ENSP_mappings:2f4w.A&PDB-ENSP_mappings:2f4w.B&PROSITE_profiles:PS50127&PANTHER:PTHR24067&PANTHER:PTHR24067:SF257&Gene3D:3.10.110.10&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000400929|protein_coding|4/6||ENST00000400929.6:c.249G>A|ENSP00000383718.2:p.Ser83%3D|464|249|83|S|tcG/tcA|rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000383718||A6NGS0.123|UPI00001D69FA|||||Gene3D:3.10.110.10&PROSITE_profiles:PS50127&PANTHER:PTHR24068&PANTHER:PTHR24068:SF135&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000400930|protein_coding|6/8||ENST00000400930.8:c.453G>A|ENSP00000383719.4:p.Ser151%3D|621|453|151|S|tcG/tcA|rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||5||CCDS15.1|ENSP00000383719|Q8N2K1.164||UPI00001D69F8|Q8N2K1-3||||PROSITE_profiles:PS50127&PANTHER:PTHR24068&PANTHER:PTHR24068:SF135&Gene3D:3.10.110.10&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000422076|protein_coding||||||||||rs375664850&COSV100230995|226|-1|cds_end_NF|SNV|HGNC|HGNC:19268||||5|||ENSP00000401898||B1AMF1.84|UPI0000E59261||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000435198|protein_coding|5/7||ENST00000435198.5:c.405G>A|ENSP00000393301.1:p.Ser135%3D|873|405|135|S|tcG/tcA|rs375664850&COSV100230995||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000393301||B1AMF0.85|UPI0000470BCD|||||Gene3D:3.10.110.10&PROSITE_profiles:PS50127&PANTHER:PTHR24067&PANTHER:PTHR24067:SF257&SMART:SM00212&Superfamily:SSF54495|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000450390|nonsense_mediated_decay|6/8||ENST00000450390.6:c.*466G>A||786|||||rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000407565||D6REN4.81|UPI0001D3BBF2||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000464036|nonsense_mediated_decay|6/8||ENST00000464036.5:c.*209G>A||726|||||rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000423880||D6RC43.61|UPI00001D69F9||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000466752|nonsense_mediated_decay|6/6||ENST00000466752.5:c.*592G>A||877|||||rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000422103||D6R9H0.82|UPI00002059A6||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|upstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000467339|processed_transcript||||||||||rs375664850&COSV100230995|666|-1||SNV|HGNC|HGNC:19268||||2||||||||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000471154|retained_intron||||||||||rs375664850&COSV100230995|121|-1||SNV|HGNC|HGNC:19268||||5||||||||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000473215|nonsense_mediated_decay|5/7||ENST00000473215.5:c.*399G>A||718|||||rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000427024||D6R9H0.82|UPI00002059A6||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000477894|nonsense_mediated_decay||||||||||rs375664850&COSV100230995|48|-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000423480||D6RA15.59|UPI0001D3BBF4||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000491779|processed_transcript|3/4||ENST00000491779.5:n.525G>A||525|||||rs375664850&COSV100230995||-1||SNV|HGNC|HGNC:19268||||2||||||||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000502382|protein_coding||||||||||rs375664850&COSV100230995|269|-1|cds_end_NF|SNV|HGNC|HGNC:19268||||4|||ENSP00000424342||D6RB84.60|UPI0001D3BBF5||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000503294|nonsense_mediated_decay||||||||||rs375664850&COSV100230995|10|-1||SNV|HGNC|HGNC:19268||||4|||ENSP00000425543||D6R9H0.82|UPI00002059A6||||||||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||,T|synonymous_variant|LOW|UBE2J2|ENSG00000160087|Transcript|ENST00000509720|protein_coding|3/5||ENST00000509720.5:c.42G>A|ENSP00000425419.2:p.Ser14%3D|333|42|14|S|tcG/tcA|rs375664850&COSV100230995||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000425419||D6RD90.61|UPI0002841248|||||Gene3D:3.10.110.10|||||||||0|0.0002326|4.07e-05|0|0|0.0001221|0.0001897|4.807e-05|3.879e-05|0|0|0.0002326|EA||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:148,5:0.038:153:61,2:60,2:126,4:107,41,4,1
chr1	1267175	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,85;MMQ=60,56;MPOS=27;POPAF=7.3;ROQ=8;TLOD=3.88;CSQ=T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000347370|protein_coding||2/6|ENST00000347370.6:c.-26+558G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000344857||A6NGS0.123|UPI00001D69FA|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000349431|protein_coding||2/6|ENST00000349431.11:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268|YES|NM_058167.3||1|P1|CCDS14.1|ENSP00000305826|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000360466|protein_coding||2/6|ENST00000360466.6:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||2|P1|CCDS14.1|ENSP00000353653|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000400929|protein_coding||1/5|ENST00000400929.6:c.-25-3789G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000383718||A6NGS0.123|UPI00001D69FA|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000400930|protein_coding||2/7|ENST00000400930.8:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||5||CCDS15.1|ENSP00000383719|Q8N2K1.164||UPI00001D69F8|Q8N2K1-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000422076|protein_coding||2/4|ENST00000422076.5:c.131+687G>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||5|||ENSP00000401898||B1AMF1.84|UPI0000E59261|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000435198|protein_coding||2/6|ENST00000435198.5:c.131+687G>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000393301||B1AMF0.85|UPI0000470BCD|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000450390|nonsense_mediated_decay||2/7|ENST00000450390.6:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000407565||D6REN4.81|UPI0001D3BBF2|||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000461142|retained_intron||2/2|ENST00000461142.3:n.303+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000464036|nonsense_mediated_decay||2/7|ENST00000464036.5:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000423880||D6RC43.61|UPI00001D69F9|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000466752|nonsense_mediated_decay||2/5|ENST00000466752.5:c.*125+558G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000422103||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000471154|retained_intron|||||||||||3606|-1||SNV|HGNC|HGNC:19268||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000473215|nonsense_mediated_decay||2/6|ENST00000473215.5:c.*125+558G>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000427024||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000477894|nonsense_mediated_decay||2/5|ENST00000477894.5:c.131+687G>A|||||||||-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000423480||D6RA15.59|UPI0001D3BBF4|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000488418|protein_coding|||||||||||687|-1|cds_end_NF|SNV|HGNC|HGNC:19268||||2|||ENSP00000427244||D6REN4.81|UPI0001D3BBF2|||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000491779|processed_transcript||1/3|ENST00000491779.5:n.292+6324G>A|||||||||-1||SNV|HGNC|HGNC:19268||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000502382|protein_coding||3/4|ENST00000502382.1:c.131+687G>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||4|||ENSP00000424342||D6RB84.60|UPI0001D3BBF5|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000503294|nonsense_mediated_decay||2/5|ENST00000503294.5:c.*125+558G>A|||||||||-1||SNV|HGNC|HGNC:19268||||4|||ENSP00000425543||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000509720|protein_coding||1/4|ENST00000509720.5:c.-129-3789G>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000425419||D6RD90.61|UPI0002841248|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1267740	.	G	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=8,3|2,0;DP=15;ECNT=1;GERMQ=45;MBQ=37,37;MFRL=231,176;MMQ=60,60;MPOS=10;POPAF=7.3;ROQ=8;TLOD=5.5;CSQ=T|5_prime_UTR_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000347370|protein_coding|2/7||ENST00000347370.6:c.-33C>A||442|||||||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000344857||A6NGS0.123|UPI00001D69FA|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000349431|protein_coding||2/6|ENST00000349431.11:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268|YES|NM_058167.3||1|P1|CCDS14.1|ENSP00000305826|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000360466|protein_coding||2/6|ENST00000360466.6:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||2|P1|CCDS14.1|ENSP00000353653|Q8N2K1.164|A0A024R075.50|UPI0000149EE7|Q8N2K1-1||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000400929|protein_coding||1/5|ENST00000400929.6:c.-25-4354C>A|||||||||-1||SNV|HGNC|HGNC:19268||||3||CCDS16.1|ENSP00000383718||A6NGS0.123|UPI00001D69FA|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000400930|protein_coding||2/7|ENST00000400930.8:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||5||CCDS15.1|ENSP00000383719|Q8N2K1.164||UPI00001D69F8|Q8N2K1-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000422076|protein_coding||2/4|ENST00000422076.5:c.131+122C>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||5|||ENSP00000401898||B1AMF1.84|UPI0000E59261|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000435198|protein_coding||2/6|ENST00000435198.5:c.131+122C>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000393301||B1AMF0.85|UPI0000470BCD|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000450390|nonsense_mediated_decay||2/7|ENST00000450390.6:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000407565||D6REN4.81|UPI0001D3BBF2|||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000461142|retained_intron||2/2|ENST00000461142.3:n.303+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000464036|nonsense_mediated_decay||2/7|ENST00000464036.5:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000423880||D6RC43.61|UPI00001D69F9|||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000466752|nonsense_mediated_decay|2/6||ENST00000466752.5:c.*118C>A||403|||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000422103||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000471154|retained_intron|||||||||||4171|-1||SNV|HGNC|HGNC:19268||||5|||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000473215|nonsense_mediated_decay|2/7||ENST00000473215.5:c.*118C>A||437|||||||-1||SNV|HGNC|HGNC:19268||||3|||ENSP00000427024||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000477894|nonsense_mediated_decay||2/5|ENST00000477894.5:c.131+122C>A|||||||||-1||SNV|HGNC|HGNC:19268||||5|||ENSP00000423480||D6RA15.59|UPI0001D3BBF4|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000488418|protein_coding|||||||||||122|-1|cds_end_NF|SNV|HGNC|HGNC:19268||||2|||ENSP00000427244||D6REN4.81|UPI0001D3BBF2|||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000491779|processed_transcript||1/3|ENST00000491779.5:n.292+5759C>A|||||||||-1||SNV|HGNC|HGNC:19268||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000502382|protein_coding||3/4|ENST00000502382.1:c.131+122C>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||4|||ENSP00000424342||D6RB84.60|UPI0001D3BBF5|||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000503294|nonsense_mediated_decay|2/6||ENST00000503294.5:c.*118C>A||421|||||||-1||SNV|HGNC|HGNC:19268||||4|||ENSP00000425543||D6R9H0.82|UPI00002059A6|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000509720|protein_coding||1/4|ENST00000509720.5:c.-129-4354C>A|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:19268||||3|||ENSP00000425419||D6RD90.61|UPI0002841248|||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918433|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:11,2:0.228:13:2,2:7,0:9,2:8,3,2,0
chr1	1285877	.	G	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=38,12|6,0;DP=78;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=130,171;MMQ=60,60;MPOS=5;POPAF=7.3;ROQ=2;TLOD=16.41;CSQ=T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||3/14|ENST00000325425.12:c.265-49G>T|||||||||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||3/14|ENST00000338555.6:c.67-49G>T|||||||||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding|||||||||||1232|1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B|||||||||||||||||||||||||||||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||5/16|ENST00000379101.8:c.465-49G>T|||||||||1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||6/17|ENST00000379116.10:c.559-49G>T|||||||||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||4/15|ENST00000400928.7:c.67-49G>T|||||||||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript|||||||||||280|1||SNV|HGNC|HGNC:10601||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding||3/3|ENST00000470022.1:c.175-49G>T|||||||||1|cds_end_NF|SNV|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:50,6:0.147:56:16,0:23,6:39,6:38,12,6,0
chr1	1286305	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=11,81|4,7;DP=117;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=143,214;MMQ=60,60;MPOS=3;POPAF=7.3;ROQ=18;TLOD=33.91;CSQ=A|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||4/14|ENST00000325425.12:c.617+27G>A|||||||||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||4/14|ENST00000338555.6:c.419+27G>A|||||||||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding|||||||||||804|1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B|||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||6/16|ENST00000379101.8:c.817+27G>A|||||||||1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF|||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||7/17|ENST00000379116.10:c.911+27G>A|||||||||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||5/15|ENST00000400928.7:c.419+27G>A|||||||||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript|||||||||||708|1||SNV|HGNC|HGNC:10601||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding|||||||||||137|1|cds_end_NF|SNV|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:92,11:0.085:103:39,5:43,2:84,7:11,81,4,7
chr1	1286678	.	G	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=34,6|2,0;DP=42;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=165,122;MMQ=60,60;MPOS=5;POPAF=7.3;ROQ=4;TLOD=3.99;CSQ=C|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||4/14|ENST00000325425.12:c.618-90G>C|||||||||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||4/14|ENST00000338555.6:c.420-90G>C|||||||||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,C|upstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding|||||||||||431|1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B|||||||||||||||||||||||||||||||||||,C|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||6/16|ENST00000379101.8:c.818-90G>C|||||||||1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF|||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||7/17|ENST00000379116.10:c.912-90G>C|||||||||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||||||||||||||||||||||||||||||||||,C|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||5/15|ENST00000400928.7:c.420-90G>C|||||||||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript|||||||||||1081|1||SNV|HGNC|HGNC:10601||||5|||||||||||||||||||||||||||||||||||||||||,C|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding|||||||||||510|1|cds_end_NF|SNV|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:40,2:0.079:42:18,0:15,2:34,2:34,6,2,0
chr1	1287462	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=102,17|6,3;DP=134;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=159,168;MMQ=60,60;MPOS=32;POPAF=2.58;ROQ=16;TLOD=15.98;CSQ=T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||6/14|ENST00000325425.12:c.1017-46C>T|||||||rs372237809||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2|||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||6/14|ENST00000338555.6:c.819-46C>T|||||||rs372237809||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1|||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||||||||||rs372237809|4929|-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3|||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding||1/6|ENST00000379099.3:c.192-46C>T|||||||rs372237809||1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B||||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||8/16|ENST00000379101.8:c.*230-46C>T|||||||rs372237809||1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF||||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||9/17|ENST00000379116.10:c.1311-46C>T|||||||rs372237809||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3|||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||7/15|ENST00000400928.7:c.819-46C>T|||||||rs372237809||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1|||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript||||||||||rs372237809|1865|1||SNV|HGNC|HGNC:10601||||5||||||||||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding||||||||||rs372237809|1294|1|cds_end_NF|SNV|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC||||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||||||||||rs372237809|4928|-1||SNV|HGNC|HGNC:16754||||1||||||||||||||0.0010|0|0|0|0.003|0.002|0.0004572|0.004081|0.0025|0.0006645|0.001194|0.0008616|0|0.001369|0.004245|0.00297|0.0004718|0.004245|gnomAD_NFE|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:119,9:0.062:128:49,2:54,4:104,6:0|1:1287462_C_T:1287462:102,17,6,3
chr1	1287464	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=105,19|3,1;DP=133;ECNT=2;GERMQ=93;MBQ=37,29;MFRL=159,176;MMQ=60,60;MPOS=27;POPAF=3.46;ROQ=5;TLOD=5.91;CSQ=T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||6/14|ENST00000325425.12:c.1017-44C>T|||||||rs180999821||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2|||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||6/14|ENST00000338555.6:c.819-44C>T|||||||rs180999821||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1|||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||||||||||rs180999821|4927|-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3|||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding||1/6|ENST00000379099.3:c.192-44C>T|||||||rs180999821||1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B||||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||8/16|ENST00000379101.8:c.*230-44C>T|||||||rs180999821||1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF||||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||9/17|ENST00000379116.10:c.1311-44C>T|||||||rs180999821||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3|||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||7/15|ENST00000400928.7:c.819-44C>T|||||||rs180999821||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1|||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript||||||||||rs180999821|1867|1||SNV|HGNC|HGNC:10601||||5||||||||||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding||||||||||rs180999821|1296|1|cds_end_NF|SNV|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC||||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||||||||||rs180999821|4926|-1||SNV|HGNC|HGNC:16754||||1||||||||||||||||||||||0.0003057|0.0002654|4.593e-05|0|0.002235|5.952e-05|0.0001412|0|6.737e-05|0.002235|gnomAD_EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:124,4:0.036:128:49,2:56,1:107,3:1|0:1287462_C_T:1287462:105,19,3,1
chr1	1290571	.	TG	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=147,147|6,3;DP=351;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=136,104;MMQ=60,60;MPOS=26;POPAF=7.3;ROQ=93;RPA=4,3;RU=G;STR;STRQ=93;TLOD=3.82;CSQ=-|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||11/14|ENST00000325425.12:c.1565+20del|||||||||1||deletion|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||11/14|ENST00000338555.6:c.1367+20del|||||||||1||deletion|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding|||||||||||2992|-1||deletion|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding|||||||||||1819|-1||deletion|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding||5/6|ENST00000379099.3:c.816+20del|||||||||1|cds_start_NF&cds_end_NF|deletion|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B|||||||||||||||||||||||||||||||||||,-|intron_variant&NMD_transcript_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||13/16|ENST00000379101.8:c.*778+20del|||||||||1||deletion|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||14/17|ENST00000379116.10:c.1859+20del|||||||||1||deletion|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||12/15|ENST00000400928.7:c.1367+20del|||||||||1||deletion|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron|||||||||||2298|-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000467651|processed_transcript|||||||||||4975|1||deletion|HGNC|HGNC:10601||||5|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000470022|protein_coding|||||||||||4404|1|cds_end_NF|deletion|HGNC|HGNC:10601||||3|||ENSP00000420548||C9JDY8.61|UPI0001B798BC|||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron|||||||||||3927|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron|||||||||||1818|-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249817|CTCF_binding_site||||||||||||||deletion|||||||||||||||||||||||||||||||||||||||||||||||,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918437|promoter_flanking_region||||||||||||||deletion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:294,9:0.024:303:87,0:81,6:242,6:0|1:1290571_TG_T:1290571:147,147,6,3
chr1	1291449	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=129,117|7,3;DP=277;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=120,168;MMQ=60,60;MPOS=8;POPAF=7.3;ROQ=13;TLOD=20.51;CSQ=T|missense_variant|MODERATE|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding|15/15||ENST00000325425.12:c.1954C>T|ENSP00000321594.8:p.Pro652Ser|2104|1954|652|P/S|Cca/Tca|||1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||tolerated(0.06)|benign(0.011)|PANTHER:PTHR11690&PANTHER:PTHR11690:SF132&TIGRFAM:TIGR00859&MobiDB_lite:mobidb-lite||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding|15/15||ENST00000338555.6:c.1756C>T|ENSP00000339504.2:p.Pro586Ser|2900|1756|586|P/S|Cca/Tca|||1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||tolerated(0.18)|benign(0.01)|PANTHER:PTHR11690&PANTHER:PTHR11690:SF132&TIGRFAM:TIGR00859&MobiDB_lite:mobidb-lite||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding|||||||||||2115|-1||SNV|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding|||||||||||942|-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript|||||||||||4987|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding|||||||||||506|1|cds_start_NF&cds_end_NF|SNV|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay|||||||||||76|1||SNV|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF|||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding|18/18||ENST00000379116.10:c.2248C>T|ENSP00000368411.5:p.Pro750Ser|2474|2248|750|P/S|Cca/Tca|||1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||deleterious(0.04)|benign(0.011)|PANTHER:PTHR11690&PANTHER:PTHR11690:SF132&MobiDB_lite:mobidb-lite&TIGRFAM:TIGR00859||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding|16/16||ENST00000400928.7:c.1756C>T|ENSP00000383717.3:p.Pro586Ser|2151|1756|586|P/S|Cca/Tca|||1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||tolerated(0.18)|benign(0.01)|PANTHER:PTHR11690&PANTHER:PTHR11690:SF132&TIGRFAM:TIGR00859&MobiDB_lite:mobidb-lite||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron|||||||||||1421|-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron|||||||||||3050|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron|||||||||||941|-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA|||||||||||4661|-1||SNV|HGNC|HGNC:50009|YES||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249817|CTCF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918437|promoter_flanking_region||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:246,10:0.045:256:63,5:90,2:212,9:129,117,7,3
chr1	1293731	.	A	ACGCCCCTGCCCTGGAGGCCC	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|1,7;DP=91;ECNT=1;GERMQ=15;MBQ=0,20;MFRL=0,216;MMQ=60,60;MPOS=96;POPAF=7.3;ROQ=93;RPA=3,4;RU=CGCCCCTGCCCTGGAGGCCC;STR;STRQ=11;TLOD=26.77;CSQ=CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||||||||||rs70949568|1707|1||insertion|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||||||||||rs70949568|1707|1||insertion|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||20/20|ENST00000353662.4:c.2136-43_2136-24dup|||||||rs70949568||-1||insertion|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||23/23|ENST00000354700.10:c.2361-43_2361-24dup|||||||rs70949568||-1||insertion|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript||||||||||rs70949568|2704|-1||insertion|HGNC|HGNC:16754||||3||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379099|protein_coding||||||||||rs70949568|2788|1|cds_start_NF&cds_end_NF|insertion|HGNC|HGNC:10601||||5|||ENSP00000368393||H0Y3F1.48|UPI000059CF4B||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379101|nonsense_mediated_decay||||||||||rs70949568|2358|1||insertion|HGNC|HGNC:10601||||1|||ENSP00000449804||F8VWH5.41|UPI00020CDFAF||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||||||||||rs70949568|1706|1||insertion|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||||||||||rs70949568|1702|1||insertion|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1|||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron||13/13|ENST00000467278.5:n.1887-43_1887-24dup|||||||rs70949568||-1||insertion|HGNC|HGNC:16754||||1||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron||||||||||rs70949568|767|-1||insertion|HGNC|HGNC:16754||||3||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||||||||||rs70949568|2734|-1||insertion|HGNC|HGNC:16754||||5||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||21/21|ENST00000492936.5:n.4001-43_4001-24dup|||||||rs70949568||-1||insertion|HGNC|HGNC:16754||||1||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000493992|retained_intron||||||||||rs70949568|4105|-1||insertion|HGNC|HGNC:16754||||5||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||,CGCCCCTGCCCTGGAGGCCC|downstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA||||||||||rs70949568|2378|-1||insertion|HGNC|HGNC:50009|YES|||||||||||||||||||||||||0.1444|0.04018|0.1817|0.02128|0.06299|0.1934|0.2565|0.25|0.072|0.2565|gnomAD_NFE|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,8:0.671:8:0,3:0,2:0,9:0,0,1,7
chr1	1296753	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,2|2,6;DP=10;ECNT=1;GERMQ=29;MBQ=37,29;MFRL=304,226;MMQ=60,60;MPOS=5;POPAF=7.3;ROQ=35;TLOD=22.43;CSQ=A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000325425|protein_coding||||||||||rs1479920310|4729|1||SNV|HGNC|HGNC:10601||||1|A2||ENSP00000321594|P51172.174||UPI000014165A|P51172-2||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000338555|protein_coding||||||||||rs1479920310|4729|1||SNV|HGNC|HGNC:10601||||2|A2||ENSP00000339504|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||12/20|ENST00000353662.4:c.1003-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||14/23|ENST00000354700.10:c.1129-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay||||||||||rs1479920310|3443|-1||SNV|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE|||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript||3/3|ENST00000379037.6:n.295-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000379116|protein_coding||||||||||rs1479920310|4728|1||SNV|HGNC|HGNC:10601|YES|NM_001130413.4||5|P2|CCDS44037.2|ENSP00000368411|P51172.174||UPI0001EF94B5|P51172-3||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|SCNN1D|ENSG00000162572|Transcript|ENST00000400928|protein_coding||||||||||rs1479920310|4724|1||SNV|HGNC|HGNC:10601||||5|A2||ENSP00000383717|P51172.174||UPI000013E180|P51172-1||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron||4/13|ENST00000467278.5:n.655-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron||||||||||rs1479920310|1745|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron||||||||||rs1479920310|1991|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||5/5|ENST00000476572.1:n.652-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000478065|retained_intron||||||||||rs1479920310|4695|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||13/21|ENST00000492936.5:n.2868-120C>T|||||||rs1479920310||-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000493992|retained_intron||||||||||rs1479920310|1084|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA||||||||||rs1479920310|583|-1||SNV|HGNC|HGNC:50009|YES||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:2,8:0.7:10:2,2:0,3:2,6:0,2,2,6
chr1	1298150	.	AC	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=19,136|2,6;DP=176;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=138,114;MMQ=60,60;MPOS=23;POPAF=7.3;ROQ=93;RPA=2,1;RU=C;STR;STRQ=93;TLOD=9.7;CSQ=-|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||10/20|ENST00000353662.4:c.790-38del|||||||||-1||deletion|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||12/23|ENST00000354700.10:c.916-38del|||||||||-1||deletion|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay|||||||||||2045|-1||deletion|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE|||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript||1/3|ENST00000379037.6:n.81+34del|||||||||-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron||2/13|ENST00000467278.5:n.442-38del|||||||||-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron|||||||||||3143|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron|||||||||||593|-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||3/5|ENST00000476572.1:n.439-38del|||||||||-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000478065|retained_intron|||||||||||3297|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron|||||||||||3705|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||11/21|ENST00000492936.5:n.2655-38del|||||||||-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000493992|retained_intron|1/2||ENST00000493992.1:n.91del||91|||||||-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA|||||||||||1981|-1||deletion|HGNC|HGNC:50009|YES||||||||||||||||||||||||||||||||||||||||||||,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344570|CTCF_binding_site||||||||||||||deletion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:155,8:0.048:163:33,3:20,0:137,6:19,136,2,6
chr1	1298712	.	AC	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=18,101|1,4;DP=152;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=134,175;MMQ=60,60;MPOS=14;POPAF=7.3;ROQ=93;RPA=4,3;RU=C;STR;STRQ=93;TLOD=4.43;CSQ=-|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||8/20|ENST00000353662.4:c.625-34del|||||||||-1||deletion|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||10/23|ENST00000354700.10:c.751-34del|||||||||-1||deletion|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay|||||||||||1483|-1||deletion|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE|||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript|||||||||||448|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000438966|processed_transcript|||||||||||4497|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|non_coding_transcript_exon_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron|1/14||ENST00000467278.5:n.243del||243|||||||-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000470659|retained_intron|||||||||||3705|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron|||||||||||31|-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||1/5|ENST00000476572.1:n.274-34del|||||||||-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000478065|retained_intron|||||||||||2735|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron|||||||||||3143|-1||deletion|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,-|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||9/21|ENST00000492936.5:n.2490-34del|||||||||-1||deletion|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000493992|retained_intron|||||||||||472|-1||deletion|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,-|upstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA|||||||||||2543|-1||deletion|HGNC|HGNC:50009|YES||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:119,5:0.045:124:22,4:25,0:101,4:18,101,1,4
chr1	1300764	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=6,42|0,2;DP=50;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=144,148;MMQ=60,60;MPOS=9;POPAF=4.31;ROQ=11;TLOD=3.73;CSQ=A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||3/20|ENST00000353662.4:c.213-72C>T|||||||rs1344875168||-1||SNV|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||5/23|ENST00000354700.10:c.339-72C>T|||||||rs1344875168||-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay||6/7|ENST00000354980.7:c.*227-72C>T|||||||rs1344875168||-1||SNV|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000379037|processed_transcript||||||||||rs1344875168|2499|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000438966|processed_transcript||||||||||rs1344875168|2446|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000467278|retained_intron||||||||||rs1344875168|1809|-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron||5/8|ENST00000472541.5:n.460-72C>T|||||||rs1344875168||-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||||||||||rs1344875168|1147|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000478065|retained_intron||||||||||rs1344875168|684|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron||||||||||rs1344875168|1092|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||4/21|ENST00000492936.5:n.2078-72C>T|||||||rs1344875168||-1||SNV|HGNC|HGNC:16754||||1|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000493992|retained_intron||||||||||rs1344875168|2523|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MIR6726|ENSG00000278073|Transcript|ENST00000613751|miRNA||||||||||rs1344875168|4594|-1||SNV|HGNC|HGNC:50009|YES||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000249818|CTCF_binding_site||||||||||rs1344875168||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001164835|TF_binding_site||||||||||rs1344875168||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:48,2:0.065:50:16,1:26,1:42,2:6,42,0,2
chr1	1304054	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=197,34|3,1;DP=252;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=125,120;MMQ=60,60;MPOS=27;POPAF=4.01;ROQ=3;TLOD=4.79;CSQ=T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000353662|protein_coding||||||||||rs1056546410|794|-1||SNV|HGNC|HGNC:16754||||1|||ENSP00000321139|Q96P50.166||UPI000012749C|Q96P50-1|||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||2/23|ENST00000354700.10:c.105+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3|||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant&NMD_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay||3/7|ENST00000354980.7:c.152+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000379031|protein_coding||||||||||rs1056546410|4543|1||SNV|HGNC|HGNC:26914|YES|NM_153339.3||1|P1|CCDS20.1|ENSP00000368318|Q8N0Z8.135||UPI0000051C19|Q8N0Z8-1|||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000438966|processed_transcript||3/3|ENST00000438966.1:n.193+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||3||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000463758|retained_intron||||||||||rs1056546410|4734|1||SNV|HGNC|HGNC:26914||||2||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000467712|protein_coding||||||||||rs1056546410|4767|1|cds_end_NF|SNV|HGNC|HGNC:26914||||5|||ENSP00000462968||J3KTG4.58|UPI0003F47FE3||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000470520|processed_transcript||||||||||rs1056546410|4557|1||SNV|HGNC|HGNC:26914||||5||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron||2/8|ENST00000472541.5:n.226+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||5||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000476572|retained_intron||||||||||rs1056546410|4437|-1||SNV|HGNC|HGNC:16754||||5||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000478065|retained_intron|1/3||ENST00000478065.5:n.848G>A||848|||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||3||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron||2/4|ENST00000479108.5:n.120+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||3||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000492936|retained_intron||1/21|ENST00000492936.5:n.1844+32G>A|||||||rs1056546410||-1||SNV|HGNC|HGNC:16754||||1||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344573|promoter||||||||||rs1056546410||||SNV||||||||||||||||||||||||||||2.612e-05|0.0001266|0|0|0|0|3.39e-05|0.0002309|0|0.0002309|gnomAD_OTH|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:231,4:0.019:235:92,2:104,1:202,3:197,34,3,1
chr1	1311463	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=7,54|2,3;DP=66;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=137,223;MMQ=60,60;MPOS=24;POPAF=7.3;ROQ=2;TLOD=4.99;CSQ=A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000323275|retained_intron|||||||||||137|-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding|||||||||||3533|-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay|||||||||||3642|-1||SNV|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE|||||||||||||||||||||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000379031|protein_coding|8/8||ENST00000379031.10:c.*84C>A||1043|||||||1||SNV|HGNC|HGNC:26914|YES|NM_153339.3||1|P1|CCDS20.1|ENSP00000368318|Q8N0Z8.135||UPI0000051C19|Q8N0Z8-1||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000411962|protein_coding|||||||||||138|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000400548||C9IYS7.94|UPI0000EE7E25|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000419704|protein_coding|||||||||||143|-1||SNV|HGNC|HGNC:26052||||2||CCDS57961.1|ENSP00000404886|Q5TA45.141|A0A024R073.53|UPI000014103F|Q5TA45-2||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000421495|protein_coding|||||||||||143|-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000464436||J3QRY6.73|UPI000048B03B|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000430786|nonsense_mediated_decay|||||||||||3415|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000404012||H7C247.38|UPI0001B798BE|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000434694|protein_coding|||||||||||2282|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000411233||C9J979.67|UPI0001F782FF|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000435064|protein_coding|||||||||||137|-1||SNV|HGNC|HGNC:26052|YES|NM_017871.6||1|P1|CCDS21.1|ENSP00000413493|Q5TA45.141||UPI00000467EC|Q5TA45-1||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000438966|processed_transcript|||||||||||3645|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000450926|protein_coding|||||||||||356|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000392848|Q5TA45.141||UPI00005A63F5|Q5TA45-3||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000458452|nonsense_mediated_decay|||||||||||143|-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000433930||E9PIS0.45|UPI0001F782F9|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000461514|retained_intron|||||||||||797|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000462432|processed_transcript|||||||||||139|-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000463758|retained_intron|||||||||||1623|1||SNV|HGNC|HGNC:26914||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000467408|retained_intron|||||||||||2083|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000467712|protein_coding|||||||||||394|1|cds_end_NF|SNV|HGNC|HGNC:26914||||5|||ENSP00000462968||J3KTG4.58|UPI0003F47FE3|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000470030|retained_intron|||||||||||122|-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000470520|processed_transcript|||||||||||435|1||SNV|HGNC|HGNC:26914||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron|||||||||||1854|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000478641|retained_intron|||||||||||143|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron|||||||||||3633|-1||SNV|HGNC|HGNC:16754||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000485710|retained_intron|||||||||||617|-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000488042|retained_intron|||||||||||2950|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000493657|retained_intron|4/4||ENST00000493657.1:n.1570C>A||1570|||||||1||SNV|HGNC|HGNC:26914||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000497304|retained_intron|||||||||||135|-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525164|retained_intron|||||||||||802|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525603|retained_intron|||||||||||4097|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525769|retained_intron|||||||||||823|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526113|retained_intron|||||||||||3541|-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526332|protein_coding|||||||||||3364|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||4|||ENSP00000434790||E9PNH9.62|UPI0001F78301|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526797|nonsense_mediated_decay|||||||||||3363|-1||SNV|HGNC|HGNC:26052||||4|||ENSP00000435418||E9PKA4.61|UPI0001F78300|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526904|retained_intron|||||||||||3683|-1||SNV|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527098|nonsense_mediated_decay|||||||||||360|-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000431952||E9PIX9.43|UPI0001F782FB|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527383|nonsense_mediated_decay|||||||||||1476|-1|cds_start_NF|SNV|HGNC|HGNC:26052||||3|||ENSP00000431425||H0YCE0.54|UPI0001F782FE|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527719|protein_coding|||||||||||3453|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000436743||E9PI75.60|UPI0001F78302|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000528879|nonsense_mediated_decay|||||||||||821|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000432777||E9PNS4.63|UPI0001F782FC|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000530031|protein_coding|||||||||||3455|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000432009||E9PIG1.59|UPI0001F78303|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531020|retained_intron|||||||||||2673|-1||SNV|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531292|retained_intron|||||||||||1596|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531377|nonsense_mediated_decay|||||||||||1324|-1|cds_start_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000433264||H0YDB1.59|UPI0001F782FD|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000532772|nonsense_mediated_decay|||||||||||164|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000431214||E9PMA2.60|UPI0001F782FA|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000533916|retained_intron|||||||||||2850|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000540437|protein_coding|||||||||||122|-1||SNV|HGNC|HGNC:26052||||2||CCDS57960.1|ENSP00000445001|Q5TA45.141||UPI0000EE7E27|Q5TA45-5||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000545578|protein_coding|||||||||||122|-1||SNV|HGNC|HGNC:26052||||2||CCDS57959.1|ENSP00000444672|Q5TA45.141||UPI00017A75B3|Q5TA45-4||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|MIR6727|ENSG00000283712|Transcript|ENST00000620702|miRNA|||||||||||1039|-1||SNV|HGNC|HGNC:50171|YES||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000620829|protein_coding|||||||||||122|-1||SNV|HGNC|HGNC:26052||||2||CCDS72678.1|ENSP00000481821||A0A087WYI0.46|UPI000014104C|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:61,5:0.056:66:27,2:27,0:54,3:7,54,2,3
chr1	1312290	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=130,100|3,1;DP=251;ECNT=2;GERMQ=93;MBQ=37,23;MFRL=122,171;MMQ=60,60;MPOS=33;POPAF=4.61;ROQ=5;TLOD=3.69;CSQ=T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000323275|retained_intron|14/16||ENST00000323275.10:n.1931G>A||1931|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||1||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354700|protein_coding||||||||||rs747481892|4360|-1||SNV|HGNC|HGNC:16754|YES|NM_030649.3||1|P1|CCDS19.2|ENSP00000346733|Q96P50.166||UPI0000050F41|Q96P50-3|||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000354980|nonsense_mediated_decay||||||||||rs747481892|4469|-1||SNV|HGNC|HGNC:16754||||5|||ENSP00000347075||F8W850.42|UPI000198C4CE||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000379031|protein_coding||||||||||rs747481892|613|1||SNV|HGNC|HGNC:26914|YES|NM_153339.3||1|P1|CCDS20.1|ENSP00000368318|Q8N0Z8.135||UPI0000051C19|Q8N0Z8-1|||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000411962|protein_coding|13/15||ENST00000411962.5:c.1249G>A|ENSP00000400548.1:p.Val417Met|1314|1249|417|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000400548||C9IYS7.94|UPI0000EE7E25|||deleterious(0.01)|benign(0.428)|PANTHER:PTHR11203&PANTHER:PTHR11203:SF37|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000419704|protein_coding|13/15||ENST00000419704.5:c.1240G>A|ENSP00000404886.1:p.Val414Met|1285|1240|414|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||2||CCDS57961.1|ENSP00000404886|Q5TA45.141|A0A024R073.53|UPI000014103F|Q5TA45-2||deleterious(0.01)|possibly_damaging(0.632)|PANTHER:PTHR11203&PANTHER:PTHR11203:SF37|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000421495|protein_coding|12/14||ENST00000421495.6:c.769G>A|ENSP00000464436.1:p.Val257Met|1355|769|257|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000464436||J3QRY6.73|UPI000048B03B|||deleterious(0.01)|possibly_damaging(0.459)|PANTHER:PTHR11203&PANTHER:PTHR11203:SF37|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000430786|nonsense_mediated_decay||||||||||rs747481892|2588|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000404012||H7C247.38|UPI0001B798BE||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000434694|protein_coding||||||||||rs747481892|1455|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000411233||C9J979.67|UPI0001F782FF||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000435064|protein_coding|15/17||ENST00000435064.6:c.1543G>A|ENSP00000413493.2:p.Val515Met|1595|1543|515|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052|YES|NM_017871.6||1|P1|CCDS21.1|ENSP00000413493|Q5TA45.141||UPI00000467EC|Q5TA45-1||deleterious(0.01)|possibly_damaging(0.459)|PDB-ENSP_mappings:5v8w.B&PDB-ENSP_mappings:5v8w.D&PDB-ENSP_mappings:5v8w.F&PDB-ENSP_mappings:5v8w.H&PDB-ENSP_mappings:7bfp.B&PDB-ENSP_mappings:7bfq.B&PDB-ENSP_mappings:7cun.K&PANTHER:PTHR11203:SF37&PANTHER:PTHR11203|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000438966|processed_transcript||||||||||rs747481892|4472|-1||SNV|HGNC|HGNC:16754||||3||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000450926|protein_coding|15/17||ENST00000450926.6:c.1477G>A|ENSP00000392848.2:p.Val493Met|1539|1477|493|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000392848|Q5TA45.141||UPI00005A63F5|Q5TA45-3||deleterious(0.01)|possibly_damaging(0.66)|PANTHER:PTHR11203:SF37&PANTHER:PTHR11203|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000458452|nonsense_mediated_decay|17/19||ENST00000458452.7:c.*1827G>A||2058|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000433930||E9PIS0.45|UPI0001F782F9||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000461514|retained_intron|4/4||ENST00000461514.6:n.883G>A||883|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000462432|processed_transcript|11/13||ENST00000462432.5:n.2346G>A||2346|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||1||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000463758|retained_intron||||||||||rs747481892|2450|1||SNV|HGNC|HGNC:26914||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000467408|retained_intron||||||||||rs747481892|1256|-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000467712|protein_coding||||||||||rs747481892|1221|1|cds_end_NF|SNV|HGNC|HGNC:26914||||5|||ENSP00000462968||J3KTG4.58|UPI0003F47FE3||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000470030|retained_intron|8/10||ENST00000470030.6:n.1835G>A||1835|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||5||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000470520|processed_transcript||||||||||rs747481892|1262|1||SNV|HGNC|HGNC:26914||||5||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron||||||||||rs747481892|2681|-1||SNV|HGNC|HGNC:16754||||5||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000478641|retained_intron|4/6||ENST00000478641.5:n.2566G>A||2566|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000479108|retained_intron||||||||||rs747481892|4460|-1||SNV|HGNC|HGNC:16754||||3||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000485710|retained_intron|6/7||ENST00000485710.5:n.751G>A||751|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||5||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000488042|retained_intron||||||||||rs747481892|2123|-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000493657|retained_intron||||||||||rs747481892|614|1||SNV|HGNC|HGNC:26914||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000497304|retained_intron|1/3||ENST00000497304.6:n.411G>A||411|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||1||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525164|retained_intron|5/5||ENST00000525164.5:n.791G>A||791|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||3||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525603|retained_intron||||||||||rs747481892|3270|-1||SNV|HGNC|HGNC:26052||||3||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525769|retained_intron|6/6||ENST00000525769.5:n.691G>A||691|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||3||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526113|retained_intron||||||||||rs747481892|2714|-1||SNV|HGNC|HGNC:26052||||5||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526332|protein_coding||||||||||rs747481892|2537|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||4|||ENSP00000434790||E9PNH9.62|UPI0001F78301||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526797|nonsense_mediated_decay||||||||||rs747481892|2536|-1||SNV|HGNC|HGNC:26052||||4|||ENSP00000435418||E9PKA4.61|UPI0001F78300||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526904|retained_intron||||||||||rs747481892|2856|-1||SNV|HGNC|HGNC:26052||||4||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527098|nonsense_mediated_decay|16/18||ENST00000527098.5:c.*1371G>A||1708|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000431952||E9PIX9.43|UPI0001F782FB||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527383|nonsense_mediated_decay||||||||||rs747481892|649|-1|cds_start_NF|SNV|HGNC|HGNC:26052||||3|||ENSP00000431425||H0YCE0.54|UPI0001F782FE||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527719|protein_coding||||||||||rs747481892|2626|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000436743||E9PI75.60|UPI0001F78302||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000528879|nonsense_mediated_decay|14/14||ENST00000528879.5:c.*641G>A||1518|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000432777||E9PNS4.63|UPI0001F782FC||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000530031|protein_coding||||||||||rs747481892|2628|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000432009||E9PIG1.59|UPI0001F78303||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531020|retained_intron||||||||||rs747481892|1846|-1||SNV|HGNC|HGNC:26052||||4||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531292|retained_intron||||||||||rs747481892|769|-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531377|nonsense_mediated_decay||||||||||rs747481892|497|-1|cds_start_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000433264||H0YDB1.59|UPI0001F782FD||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|3_prime_UTR_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000532772|nonsense_mediated_decay|11/13||ENST00000532772.5:c.*965G>A||1126|||||rs747481892||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000431214||E9PMA2.60|UPI0001F782FA||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000533916|retained_intron||||||||||rs747481892|2023|-1||SNV|HGNC|HGNC:26052||||2||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000540437|protein_coding|17/19||ENST00000540437.5:c.1561G>A|ENSP00000445001.1:p.Val521Met|2095|1561|521|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||2||CCDS57960.1|ENSP00000445001|Q5TA45.141||UPI0000EE7E27|Q5TA45-5||deleterious(0.01)|possibly_damaging(0.511)|PANTHER:PTHR11203&PANTHER:PTHR11203:SF37|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000545578|protein_coding|16/18||ENST00000545578.5:c.1456G>A|ENSP00000444672.1:p.Val486Met|1729|1456|486|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||2||CCDS57959.1|ENSP00000444672|Q5TA45.141||UPI00017A75B3|Q5TA45-4||deleterious(0.01)|possibly_damaging(0.459)|PANTHER:PTHR11203&PANTHER:PTHR11203:SF37|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|MIR6727|ENSG00000283712|Transcript|ENST00000620702|miRNA||||||||||rs747481892|212|-1||SNV|HGNC|HGNC:50171|YES|||||||||||||||||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|INTS11|ENSG00000127054|Transcript|ENST00000620829|protein_coding|13/15||ENST00000620829.4:c.1249G>A|ENSP00000481821.1:p.Val417Met|1328|1249|417|V/M|Gtg/Atg|rs747481892||-1||SNV|HGNC|HGNC:26052||||2||CCDS72678.1|ENSP00000481821||A0A087WYI0.46|UPI000014104C|||deleterious(0.01)|possibly_damaging(0.694)|PANTHER:PTHR11203:SF37&PANTHER:PTHR11203|||||||||||1.915e-05|0|4.033e-05|0|8.718e-05|0|1.659e-05|0|0|8.718e-05|gnomAD_EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:230,4:0.02:234:57,2:81,1:194,3:130,100,3,1
chr1	1314368	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=175,333|4,4;DP=543;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=119,79;MMQ=60,60;MPOS=9;POPAF=7.3;ROQ=15;TLOD=6.41;CSQ=A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000323275|retained_intron||6/15|ENST00000323275.10:n.1091-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000379031|protein_coding|||||||||||2691|1||SNV|HGNC|HGNC:26914|YES|NM_153339.3||1|P1|CCDS20.1|ENSP00000368318|Q8N0Z8.135||UPI0000051C19|Q8N0Z8-1||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000411962|protein_coding||5/14|ENST00000411962.5:c.409-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000400548||C9IYS7.94|UPI0000EE7E25|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000419704|protein_coding||5/14|ENST00000419704.5:c.400-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2||CCDS57961.1|ENSP00000404886|Q5TA45.141|A0A024R073.53|UPI000014103F|Q5TA45-2||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000421495|protein_coding||4/13|ENST00000421495.6:c.-256-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000464436||J3QRY6.73|UPI000048B03B|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000429572|protein_coding|||||||||||4311|-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000481275||A0A087WXT8.41|UPI0001638EEF|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000430786|nonsense_mediated_decay|||||||||||510|-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000404012||H7C247.38|UPI0001B798BE|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000434694|protein_coding||5/6|ENST00000434694.6:c.793-3C>T|||||||||-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000411233||C9J979.67|UPI0001F782FF|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000435064|protein_coding||7/16|ENST00000435064.6:c.703-3C>T|||||||||-1||SNV|HGNC|HGNC:26052|YES|NM_017871.6||1|P1|CCDS21.1|ENSP00000413493|Q5TA45.141||UPI00000467EC|Q5TA45-1||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000240731|Transcript|ENST00000444968|lncRNA|||||||||||3213|-1||SNV|||YES|||3|||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000450926|protein_coding||7/16|ENST00000450926.6:c.637-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000392848|Q5TA45.141||UPI00005A63F5|Q5TA45-3||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000458452|nonsense_mediated_decay||9/18|ENST00000458452.7:c.*987-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000433930||E9PIS0.45|UPI0001F782F9|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000461514|retained_intron|||||||||||588|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000462432|processed_transcript||4/12|ENST00000462432.5:n.1568-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000463758|retained_intron|||||||||||4528|1||SNV|HGNC|HGNC:26914||||2|||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000467408|retained_intron||2/4|ENST00000467408.6:n.338-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000467712|protein_coding|||||||||||3299|1|cds_end_NF|SNV|HGNC|HGNC:26914||||5|||ENSP00000462968||J3KTG4.58|UPI0003F47FE3|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000470030|retained_intron||1/9|ENST00000470030.6:n.611-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000470520|processed_transcript|||||||||||3340|1||SNV|HGNC|HGNC:26914||||5|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ACAP3|ENSG00000131584|Transcript|ENST00000472541|retained_intron|||||||||||4759|-1||SNV|HGNC|HGNC:16754||||5|||||||||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000478641|retained_intron|1/6||ENST00000478641.5:n.803C>T||803|||||||-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000485710|retained_intron|||||||||||543|-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000488042|retained_intron|||||||||||45|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000493534|processed_transcript|||||||||||4692|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|PUSL1|ENSG00000169972|Transcript|ENST00000493657|retained_intron|||||||||||2692|1||SNV|HGNC|HGNC:26914||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000496353|retained_intron|||||||||||4329|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000497304|retained_intron|||||||||||1668|-1||SNV|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000498173|retained_intron|||||||||||4313|-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525164|retained_intron|||||||||||603|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525603|retained_intron|||||||||||1192|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525769|retained_intron|||||||||||618|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526113|retained_intron|||||||||||636|-1||SNV|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526332|protein_coding|||||||||||459|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||4|||ENSP00000434790||E9PNH9.62|UPI0001F78301|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526797|nonsense_mediated_decay|||||||||||458|-1||SNV|HGNC|HGNC:26052||||4|||ENSP00000435418||E9PKA4.61|UPI0001F78300|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526904|retained_intron|||||||||||778|-1||SNV|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000527098|nonsense_mediated_decay||8/17|ENST00000527098.5:c.*531-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2|||ENSP00000431952||E9PIX9.43|UPI0001F782FB|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000527383|nonsense_mediated_decay||2/6|ENST00000527383.5:c.*125-3C>T|||||||||-1|cds_start_NF|SNV|HGNC|HGNC:26052||||3|||ENSP00000431425||H0YCE0.54|UPI0001F782FE|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527719|protein_coding|||||||||||548|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000436743||E9PI75.60|UPI0001F78302|||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000528879|nonsense_mediated_decay||7/13|ENST00000528879.5:c.703-447C>T|||||||||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000432777||E9PNS4.63|UPI0001F782FC|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000530031|protein_coding|||||||||||550|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000432009||E9PIG1.59|UPI0001F78303|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000531020|retained_intron||1/1|ENST00000531020.1:n.319-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531292|retained_intron|1/4||ENST00000531292.5:n.297C>T||297|||||||-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|intron_variant&NMD_transcript_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531377|nonsense_mediated_decay||3/6|ENST00000531377.5:c.*125-447C>T|||||||||-1|cds_start_NF|SNV|HGNC|HGNC:26052||||5|||ENSP00000433264||H0YDB1.59|UPI0001F782FD|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&NMD_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000532772|nonsense_mediated_decay||3/12|ENST00000532772.5:c.*125-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||5|||ENSP00000431214||E9PMA2.60|UPI0001F782FA|||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000532952|processed_transcript|||||||||||4979|-1||SNV|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000533916|retained_intron||3/3|ENST00000533916.5:n.353-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000534345|protein_coding|||||||||||4938|-1|cds_end_NF|SNV|HGNC|HGNC:26052||||4|||ENSP00000435772||E9PIL7.59|UPI0001F78304|||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000540437|protein_coding||9/18|ENST00000540437.5:c.721-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2||CCDS57960.1|ENSP00000445001|Q5TA45.141||UPI0000EE7E27|Q5TA45-5||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000545578|protein_coding||8/17|ENST00000545578.5:c.616-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2||CCDS57959.1|ENSP00000444672|Q5TA45.141||UPI00017A75B3|Q5TA45-4||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MIR6727|ENSG00000283712|Transcript|ENST00000620702|miRNA|||||||||||1802|-1||SNV|HGNC|HGNC:50171|YES||||||||||||||||||||||||||||||||||||||||||||,A|splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant|LOW|INTS11|ENSG00000127054|Transcript|ENST00000620829|protein_coding||5/14|ENST00000620829.4:c.409-3C>T|||||||||-1||SNV|HGNC|HGNC:26052||||2||CCDS72678.1|ENSP00000481821||A0A087WYI0.46|UPI000014104C|||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344576|TF_binding_site||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:508,8:0.012:516:186,2:208,2:415,4:175,333,4,4
chr1	1324790	.	GT	AG	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,6;DP=6;ECNT=1;GERMQ=43;MBQ=0,37;MFRL=0,255;MMQ=60,60;MPOS=3;POPAF=7.3;ROQ=54;TLOD=21.97;CSQ=AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000323275|retained_intron|||||||||||169|-1||substitution|HGNC|HGNC:26052||||1|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000343938|protein_coding|||||||||||11|1||substitution|HGNC|HGNC:28116|YES|NM_001029885.2||2|P1|CCDS30555.1|ENSP00000343890|Q5TA50.121|S4S694.44|UPI00001AF6EA|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000411962|protein_coding|||||||||||117|-1||substitution|HGNC|HGNC:26052||||5|||ENSP00000400548||C9IYS7.94|UPI0000EE7E25|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000419704|protein_coding|||||||||||137|-1||substitution|HGNC|HGNC:26052||||2||CCDS57961.1|ENSP00000404886|Q5TA45.141|A0A024R073.53|UPI000014103F|Q5TA45-2||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000421495|protein_coding|||||||||||153|-1||substitution|HGNC|HGNC:26052||||2|||ENSP00000464436||J3QRY6.73|UPI000048B03B|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000429572|protein_coding|||||||||||124|-1||substitution|HGNC|HGNC:26052||||2|||ENSP00000481275||A0A087WXT8.41|UPI0001638EEF|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000430786|nonsense_mediated_decay|||||||||||165|-1||substitution|HGNC|HGNC:26052||||5|||ENSP00000404012||H7C247.38|UPI0001B798BE|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000434694|protein_coding|||||||||||160|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||5|||ENSP00000411233||C9J979.67|UPI0001F782FF|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000435064|protein_coding|||||||||||130|-1||substitution|HGNC|HGNC:26052|YES|NM_017871.6||1|P1|CCDS21.1|ENSP00000413493|Q5TA45.141||UPI00000467EC|Q5TA45-1||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000450926|protein_coding|||||||||||120|-1||substitution|HGNC|HGNC:26052||||5|||ENSP00000392848|Q5TA45.141||UPI00005A63F5|Q5TA45-3||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000458452|nonsense_mediated_decay|||||||||||140|-1||substitution|HGNC|HGNC:26052||||2|||ENSP00000433930||E9PIS0.45|UPI0001F782F9|||||||||||||||||||||||||||||||||||,AG|non_coding_transcript_exon_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000464957|processed_transcript|1/2||ENST00000464957.1:n.35_36delinsAG||35-36|||||||1||substitution|HGNC|HGNC:28116||||2|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000470679|nonsense_mediated_decay|||||||||||187|-1|cds_start_NF|substitution|HGNC|HGNC:26052||||5|||ENSP00000434782||H0YE15.56|UPI0001F78307|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000488011|protein_coding|||||||||||450|1|cds_end_NF|substitution|HGNC|HGNC:28116||||2|||ENSP00000462636||J3KST3.58|UPI0003F4844A|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000488042|retained_intron|||||||||||161|-1||substitution|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000490853|processed_transcript|||||||||||141|-1||substitution|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000493534|processed_transcript|||||||||||132|-1||substitution|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000496353|retained_intron|||||||||||179|-1||substitution|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000498173|retained_intron|||||||||||103|-1||substitution|HGNC|HGNC:26052||||2|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000498476|protein_coding|||||||||||130|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||4|||ENSP00000436824||E9PQF0.59|UPI0001F78306|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525285|nonsense_mediated_decay|||||||||||177|-1|cds_start_NF|substitution|HGNC|HGNC:26052||||4|||ENSP00000436396||H0YEQ9.39|UPI0001F78308|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000525603|retained_intron|||||||||||3885|-1||substitution|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526113|retained_intron|||||||||||153|-1||substitution|HGNC|HGNC:26052||||5|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526332|protein_coding|||||||||||130|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||4|||ENSP00000434790||E9PNH9.62|UPI0001F78301|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526797|nonsense_mediated_decay|||||||||||132|-1||substitution|HGNC|HGNC:26052||||4|||ENSP00000435418||E9PKA4.61|UPI0001F78300|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000526904|retained_intron|||||||||||132|-1||substitution|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527098|nonsense_mediated_decay|||||||||||124|-1||substitution|HGNC|HGNC:26052||||2|||ENSP00000431952||E9PIX9.43|UPI0001F782FB|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000527719|protein_coding|||||||||||119|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||5|||ENSP00000436743||E9PI75.60|UPI0001F78302|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000528879|nonsense_mediated_decay|||||||||||142|-1||substitution|HGNC|HGNC:26052||||5|||ENSP00000432777||E9PNS4.63|UPI0001F782FC|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000530031|protein_coding|||||||||||131|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||5|||ENSP00000432009||E9PIG1.59|UPI0001F78303|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000530233|retained_intron|||||||||||132|-1||substitution|HGNC|HGNC:26052||||4|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000531019|nonsense_mediated_decay|||||||||||130|-1||substitution|HGNC|HGNC:26052||||4|||ENSP00000433733||E9PJG0.60|UPI0001F78305|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000532772|nonsense_mediated_decay|||||||||||162|-1||substitution|HGNC|HGNC:26052||||5|||ENSP00000431214||E9PMA2.60|UPI0001F782FA|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000532952|processed_transcript|||||||||||148|-1||substitution|HGNC|HGNC:26052||||3|||||||||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000534345|protein_coding|||||||||||119|-1|cds_end_NF|substitution|HGNC|HGNC:26052||||4|||ENSP00000435772||E9PIL7.59|UPI0001F78304|||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000540437|protein_coding|||||||||||103|-1||substitution|HGNC|HGNC:26052||||2||CCDS57960.1|ENSP00000445001|Q5TA45.141||UPI0000EE7E27|Q5TA45-5||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000545578|protein_coding|||||||||||103|-1||substitution|HGNC|HGNC:26052||||2||CCDS57959.1|ENSP00000444672|Q5TA45.141||UPI00017A75B3|Q5TA45-4||||||||||||||||||||||||||||||||||,AG|upstream_gene_variant|MODIFIER|INTS11|ENSG00000127054|Transcript|ENST00000620829|protein_coding|||||||||||103|-1||substitution|HGNC|HGNC:26052||||2||CCDS72678.1|ENSP00000481821||A0A087WYI0.46|UPI000014104C|||||||||||||||||||||||||||||||||||,AG|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000178|promoter||||||||||||||substitution|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,6:0.869:6:0,4:0,2:0,6:0,0,0,6
chr1	1331483	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=80,109|1,5;DP=214;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=126,134;MMQ=60,60;MPOS=2;POPAF=3.83;ROQ=2;TLOD=10.31;CSQ=T|synonymous_variant|LOW|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding|1/6||ENST00000339381.6:c.138C>T|ENSP00000344411.5:p.Ala46%3D|204|138|46|A|gcC/gcT|rs372727451||1||SNV|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47|||||CDD:cd06363&PANTHER:PTHR24061:SF435&PANTHER:PTHR24061&Gene3D:3.40.50.2300&Superfamily:SSF53822|||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000343938|protein_coding||||||||||rs372727451|2587|1||SNV|HGNC|HGNC:28116|YES|NM_001029885.2||2|P1|CCDS30555.1|ENSP00000343890|Q5TA50.121|S4S694.44|UPI00001AF6EA||||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding||||||||||rs372727451|3795|-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding||||||||||rs372727451|3793|-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000464957|processed_transcript||||||||||rs372727451|3489|1||SNV|HGNC|HGNC:28116||||2||||||||||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000488011|protein_coding||||||||||rs372727451|4012|1|cds_end_NF|SNV|HGNC|HGNC:28116||||2|||ENSP00000462636||J3KST3.58|UPI0003F4844A||||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding||||||||||rs372727451|4929|-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918445|promoter_flanking_region||||||||||rs372727451||||SNV||||||||||||||||||||0.0002|0|0|0.001|0|0|||0.0002253|0|0|0|0.00263|0|2.935e-05|0|0.0001349|0.00263|gnomAD_EAS|benign||1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:189,6:0.035:195:76,4:81,1:165,5:80,109,1,5
chr1	1333592	.	GC	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=179,217|2,5;DP=426;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=129,163;MMQ=60,60;MPOS=52;POPAF=7.3;ROQ=93;TLOD=4.53;CSQ=-|frameshift_variant|HIGH|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding|6/6||ENST00000339381.6:c.1688del|ENSP00000344411.5:p.Ala563AspfsTer14|1754|1688|563|A/X|gCa/ga|||1||deletion|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47|||||PANTHER:PTHR24061:SF435&PANTHER:PTHR24061&Gene3D:2.10.50.30||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|CPTP|ENSG00000224051|Transcript|ENST00000343938|protein_coding|||||||||||4697|1||deletion|HGNC|HGNC:28116|YES|NM_001029885.2||2|P1|CCDS30555.1|ENSP00000343890|Q5TA50.121|S4S694.44|UPI00001AF6EA|||||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|||||||||||1685|-1||deletion|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding|||||||||||1683|-1||deletion|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding|||||||||||3430|-1|cds_start_NF|deletion|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1|||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding|||||||||||2819|-1|cds_start_NF|deletion|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1|||||||||||||||||||||||||||||||||,-|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron|||||||||||4741|-1||deletion|HGNC|HGNC:3084||||5||||||||1|||||||||||||||||||||||||||||||||,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000918445|promoter_flanking_region||||||||||||||deletion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:396,7:0.015:403:91,2:94,0:326,5:179,217,2,5
chr1	1336588	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=2,26|0,2;DP=31;ECNT=1;GERMQ=63;MBQ=37,37;MFRL=159,150;MMQ=60,60;MPOS=20;POPAF=4.61;ROQ=12;TLOD=4.31;CSQ=A|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding||||||||||rs539565104|1274|1||SNV|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47|||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding||14/14|ENST00000378888.10:c.1715-73C>T|||||||rs539565104||-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding||14/14|ENST00000378891.9:c.1640-73C>T|||||||rs539565104||-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|Transcript|ENST00000616525|miRNA||||||||||rs539565104|3062|-1||SNV|HGNC|HGNC:50046|YES||||||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding||||||||||rs539565104|435|-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1|||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding||5/5|ENST00000632445.1:c.*28-73C>T|||||||rs539565104||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000633096|retained_intron||||||||||rs539565104|2904|-1||SNV|HGNC|HGNC:3084||||4||||||||1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron||||||||||rs539565104|1746|-1||SNV|HGNC|HGNC:3084||||5||||||||1|||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:28,2:0.1:30:12,1:14,1:26,2:2,26,0,2
chr1	1337030	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=178,96|2,3;DP=285;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=138,134;MMQ=60,60;MPOS=16;POPAF=7.3;ROQ=5;TLOD=6.91;CSQ=T|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding||||||||||rs1027260386|1716|1||SNV|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47|||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding||14/14|ENST00000378888.10:c.1715-515G>A|||||||rs1027260386||-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding||14/14|ENST00000378891.9:c.1640-515G>A|||||||rs1027260386||-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000472445|retained_intron||||||||||rs1027260386|4740|-1||SNV|HGNC|HGNC:3084||||2||||||||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|Transcript|ENST00000616525|miRNA||||||||||rs1027260386|2620|-1||SNV|HGNC|HGNC:50046|YES||||||||||||||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding|8/8||ENST00000631679.1:c.*15G>A||771|||||rs1027260386||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1|||||||||||||||||||||||||||||||||,T|3_prime_UTR_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding|5/6||ENST00000632445.1:c.*15G>A||669|||||rs1027260386||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000633096|retained_intron||||||||||rs1027260386|2462|-1||SNV|HGNC|HGNC:3084||||4||||||||1|||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron||||||||||rs1027260386|1304|-1||SNV|HGNC|HGNC:3084||||5||||||||1|||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:274,5:0.02:279:101,1:85,1:240,4:1|0:1337018_C_T:1337018:178,96,2,3
chr1	1339367	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=230,321|3,6;DP=579;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=119,152;MMQ=60,60;MPOS=2;POPAF=7.3;ROQ=8;TLOD=12.33;CSQ=T|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding||||||||||rs764290807|4053|1||SNV|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47||||||||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|11/15||ENST00000378888.10:c.1127G>A|ENSP00000368166.5:p.Arg376His|1480|1127|376|R/H|cGc/cAc|rs764290807||-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|tolerated(0.48)|benign(0.009)|PANTHER:PTHR10878&PANTHER:PTHR10878:SF5|||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding|11/15||ENST00000378891.9:c.1127G>A|ENSP00000368169.5:p.Arg376His|1174|1127|376|R/H|cGc/cAc|rs764290807||-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|tolerated(0.24)|benign(0.006)|Gene3D:1.10.10.10&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5|||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000472445|retained_intron||||||||||rs764290807|2403|-1||SNV|HGNC|HGNC:3084||||2||||||||1||||||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|Transcript|ENST00000616525|miRNA||||||||||rs764290807|283|-1||SNV|HGNC|HGNC:50046|YES|||||||||||||||||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding|4/8||ENST00000631679.1:c.233G>A|ENSP00000488181.1:p.Arg78His|233|233|78|R/H|cGc/cAc|rs764290807||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1|tolerated(0.32)|benign(0.018)|Gene3D:1.10.10.10&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5|||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding|1/6||ENST00000632445.1:c.56G>A|ENSP00000488888.1:p.Arg19His|56|56|19|R/H|cGc/cAc|rs764290807||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1|tolerated(0.67)|benign(0.03)|PANTHER:PTHR10878&PANTHER:PTHR10878:SF5|||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000633096|retained_intron||||||||||rs764290807|125|-1||SNV|HGNC|HGNC:3084||||4||||||||1||||||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron|3/5||ENST00000634054.1:n.513G>A||513|||||rs764290807||-1||SNV|HGNC|HGNC:3084||||5||||||||1||||||||||||||2.586e-05|0|0|0|9.046e-05|0|5.05e-05|0|0|9.046e-05|gnomAD_EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:551,9:0.017:560:207,2:237,5:469,8:0|1:1339367_C_T:1339367:230,321,3,6
chr1	1339610	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=83,49|3,1;DP=150;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=124,122;MMQ=60,60;MPOS=26;POPAF=7.3;ROQ=6;TLOD=5.83;CSQ=T|downstream_gene_variant|MODIFIER|TAS1R3|ENSG00000169962|Transcript|ENST00000339381|protein_coding||||||||||rs753965150|4296|1||SNV|HGNC|HGNC:15661|YES|NM_152228.3||2|P1|CCDS30556.1|ENSP00000344411|Q7RTX0.162||UPI0000051F47||||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|synonymous_variant|LOW|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|10/15||ENST00000378888.10:c.1026G>A|ENSP00000368166.5:p.Thr342%3D|1379|1026|342|T|acG/acA|rs753965150||-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||Gene3D:2.30.42.10&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5&Superfamily:SSF50156|||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|synonymous_variant|LOW|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding|10/15||ENST00000378891.9:c.1026G>A|ENSP00000368169.5:p.Thr342%3D|1073|1026|342|T|acG/acA|rs753965150||-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|||Gene3D:2.30.42.10&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5&Superfamily:SSF50156|||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000472445|retained_intron||||||||||rs753965150|2160|-1||SNV|HGNC|HGNC:3084||||2||||||||1||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|downstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|Transcript|ENST00000616525|miRNA||||||||||rs753965150|40|-1||SNV|HGNC|HGNC:50046|YES|||||||||||||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|synonymous_variant|LOW|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding|3/8||ENST00000631679.1:c.132G>A|ENSP00000488181.1:p.Thr44%3D|132|132|44|T|acG/acA|rs753965150||-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1|||Gene3D:2.30.42.10&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5&Superfamily:SSF50156|||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding||||||||||rs753965150|188|-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000633096|retained_intron|3/3||ENST00000633096.1:n.462G>A||462|||||rs753965150||-1||SNV|HGNC|HGNC:3084||||4||||||||1||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron|3/5||ENST00000634054.1:n.270G>A||270|||||rs753965150||-1||SNV|HGNC|HGNC:3084||||5||||||||1||||||||||||||4.063e-06|0|0|0|0|0|9.043e-06|0|0|9.043e-06|gnomAD_NFE|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:132,4:0.034:136:39,1:62,2:111,3:83,49,3,1
chr1	1340417	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=206,185|4,4;DP=417;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=126,136;MMQ=60,60;MPOS=63;POPAF=7.3;ROQ=2;TLOD=8.51;CSQ=A|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|6/15||ENST00000378888.10:c.692C>T|ENSP00000368166.5:p.Ala231Val|1045|692|231|A/V|gCg/gTg|rs200649758||-1||SNV|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|tolerated(0.35)|benign(0)|Pfam:PF02377&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5&MobiDB_lite:mobidb-lite|||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|missense_variant|MODERATE|DVL1|ENSG00000107404|Transcript|ENST00000378891|protein_coding|6/15||ENST00000378891.9:c.692C>T|ENSP00000368169.5:p.Ala231Val|739|692|231|A/V|gCg/gTg|rs200649758||-1||SNV|HGNC|HGNC:3084||||1||CCDS22.1|ENSP00000368169|O14640.208||UPI000013D455|O14640-2|1|tolerated(0.27)|benign(0)|Pfam:PF02377&PANTHER:PTHR10878&PANTHER:PTHR10878:SF5&MobiDB_lite:mobidb-lite|||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|downstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000472445|retained_intron||||||||||rs200649758|1353|-1||SNV|HGNC|HGNC:3084||||2||||||||1||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|upstream_gene_variant|MODIFIER|MIR6808|ENSG00000284372|Transcript|ENST00000616525|miRNA||||||||||rs200649758|709|-1||SNV|HGNC|HGNC:50046|YES|||||||||||||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000631679|protein_coding||||||||||rs200649758|365|-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488181||A0A0J9YWZ5.30|UPI000645474F||1||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000632445|protein_coding||||||||||rs200649758|995|-1|cds_start_NF|SNV|HGNC|HGNC:3084||||5|||ENSP00000488888||A0A0J9YYK1.30|UPI00064546A2||1||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000633096|retained_intron||||||||||rs200649758|52|-1||SNV|HGNC|HGNC:3084||||4||||||||1||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||,A|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000634054|retained_intron||||||||||rs200649758|227|-1||SNV|HGNC|HGNC:3084||||5||||||||1||||||||||||||2.139e-05|0|0.0001224|0|5.821e-05|0|0|0|0|0.0001224|gnomAD_AMR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:391,8:0.015:399:156,3:168,1:334,4:206,185,4,4
chr1	1354171	.	G	GTGCCCCCCTCCC	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=42,78|0,3;DP=123;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=143,115;MMQ=60,60;MPOS=22;POPAF=7.3;ROQ=93;TLOD=5.98;CSQ=TGCCCCCCTCCC|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000309212|protein_coding||7/9|ENST00000309212.11:c.1145+21_1145+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542|YES|NM_032348.4||1|P2|CCDS24.1|ENSP00000307887|Q9BRK3.164||UPI000003ED26|Q9BRK3-1||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000342753|protein_coding||6/8|ENST00000342753.8:c.842+21_842+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||1||CCDS59950.1|ENSP00000344998|Q9BRK3.164||UPI00001A7404|Q9BRK3-4||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|||||||||||4753|-1||insertion|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000445648|protein_coding||7/9|ENST00000445648.5:c.1145+21_1145+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||2|A2|CCDS59951.1|ENSP00000399229|Q9BRK3.164||UPI0000470B85|Q9BRK3-2||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|downstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000460473|retained_intron|||||||||||911|-1||insertion|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|downstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000464351|retained_intron|||||||||||832|-1||insertion|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000473097|retained_intron||2/3|ENST00000473097.5:n.161+21_161+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000474033|retained_intron||1/3|ENST00000474033.5:n.72+21_72+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||1|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000476718|retained_intron||2/4|ENST00000476718.1:n.652+21_652+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding||7/9|ENST00000477278.3:c.1118+21_1118+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||5|A2|CCDS59952.1|ENSP00000436135|Q9BRK3.164||UPI000013E183|Q9BRK3-3||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000478517|retained_intron||1/2|ENST00000478517.5:n.55+21_55+22insGGGAGGGGGGCA|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,TGCCCCCCTCCC|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344595|promoter||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:120,3:0.035:123:26,0:35,0:111,3:0|1:1354171_G_GTGCCCCCCTCCC:1354171:42,78,0,3
chr1	1354175	.	C	CCTCCT	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=44,80|0,3;DP=132;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=143,115;MMQ=60,60;MPOS=6;POPAF=7.3;ROQ=93;TLOD=5.92;CSQ=CTCCT|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000309212|protein_coding||7/9|ENST00000309212.11:c.1145+17_1145+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542|YES|NM_032348.4||1|P2|CCDS24.1|ENSP00000307887|Q9BRK3.164||UPI000003ED26|Q9BRK3-1||||||||||||||||||||||||||||||||||,CTCCT|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000342753|protein_coding||6/8|ENST00000342753.8:c.842+17_842+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||1||CCDS59950.1|ENSP00000344998|Q9BRK3.164||UPI00001A7404|Q9BRK3-4||||||||||||||||||||||||||||||||||,CTCCT|upstream_gene_variant|MODIFIER|DVL1|ENSG00000107404|Transcript|ENST00000378888|protein_coding|||||||||||4757|-1||insertion|HGNC|HGNC:3084|YES|NM_001330311.2||5|P1|CCDS81252.1|ENSP00000368166|O14640.208||UPI00001AF922|O14640-1|1|||||||||||||||||||||||||||||||||,CTCCT|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000445648|protein_coding||7/9|ENST00000445648.5:c.1145+17_1145+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||2|A2|CCDS59951.1|ENSP00000399229|Q9BRK3.164||UPI0000470B85|Q9BRK3-2||||||||||||||||||||||||||||||||||,CTCCT|downstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000460473|retained_intron|||||||||||907|-1||insertion|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,CTCCT|downstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000464351|retained_intron|||||||||||828|-1||insertion|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,CTCCT|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000473097|retained_intron||2/3|ENST00000473097.5:n.161+17_161+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,CTCCT|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000474033|retained_intron||1/3|ENST00000474033.5:n.72+17_72+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||1|||||||||||||||||||||||||||||||||||||||||,CTCCT|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000476718|retained_intron||2/4|ENST00000476718.1:n.652+17_652+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,CTCCT|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding||7/9|ENST00000477278.3:c.1118+17_1118+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||5|A2|CCDS59952.1|ENSP00000436135|Q9BRK3.164||UPI000013E183|Q9BRK3-3||||||||||||||||||||||||||||||||||,CTCCT|intron_variant&non_coding_transcript_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000478517|retained_intron||1/2|ENST00000478517.5:n.55+17_55+18insAGGAG|||||||||-1||insertion|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,CTCCT|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344595|promoter||||||||||||||insertion|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:124,3:0.035:127:27,0:33,0:115,3:0|1:1354171_G_GTGCCCCCCTCCC:1354171:44,80,0,3
chr1	1355492	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=111,56|3,1;DP=179;ECNT=1;GERMQ=93;MBQ=37,29;MFRL=121,136;MMQ=60,60;MPOS=11;POPAF=7.3;ROQ=6;TLOD=5.36;CSQ=T|missense_variant|MODERATE|MXRA8|ENSG00000162576|Transcript|ENST00000309212|protein_coding|3/10||ENST00000309212.11:c.334G>A|ENSP00000307887.6:p.Ala112Thr|385|334|112|A/T|Gcc/Acc|||-1||SNV|HGNC|HGNC:7542|YES|NM_032348.4||1|P2|CCDS24.1|ENSP00000307887|Q9BRK3.164||UPI000003ED26|Q9BRK3-1||deleterious(0.05)|benign(0.007)|Gene3D:2.60.40.10&PDB-ENSP_mappings:6jo8.M&PDB-ENSP_mappings:6jo8.N&PDB-ENSP_mappings:6jo8.O&Pfam:PF07686&PROSITE_profiles:PS50835&PANTHER:PTHR44793&SMART:SM00406&SMART:SM00409&Superfamily:SSF48726||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000342753|protein_coding||2/8|ENST00000342753.8:c.74-147G>A|||||||||-1||SNV|HGNC|HGNC:7542||||1||CCDS59950.1|ENSP00000344998|Q9BRK3.164||UPI00001A7404|Q9BRK3-4||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|MXRA8|ENSG00000162576|Transcript|ENST00000445648|protein_coding|3/10||ENST00000445648.5:c.334G>A|ENSP00000399229.2:p.Ala112Thr|373|334|112|A/T|Gcc/Acc|||-1||SNV|HGNC|HGNC:7542||||2|A2|CCDS59951.1|ENSP00000399229|Q9BRK3.164||UPI0000470B85|Q9BRK3-2||deleterious(0.05)|benign(0.003)|PROSITE_profiles:PS50835&PANTHER:PTHR44793&Gene3D:2.60.40.10&Pfam:PF07686&SMART:SM00406&SMART:SM00409&Superfamily:SSF48726||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000460473|retained_intron|1/2||ENST00000460473.1:n.21G>A||21|||||||-1||SNV|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,T|non_coding_transcript_exon_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000464351|retained_intron|1/2||ENST00000464351.1:n.21G>A||21|||||||-1||SNV|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000473097|retained_intron|||||||||||1018|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000474033|retained_intron|||||||||||1228|-1||SNV|HGNC|HGNC:7542||||1|||||||||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000476718|retained_intron|||||||||||476|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,T|missense_variant|MODERATE|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding|3/10||ENST00000477278.3:c.307G>A|ENSP00000436135.1:p.Ala103Thr|821|307|103|A/T|Gcc/Acc|||-1||SNV|HGNC|HGNC:7542||||5|A2|CCDS59952.1|ENSP00000436135|Q9BRK3.164||UPI000013E183|Q9BRK3-3||tolerated(0.05)|benign(0.007)|Gene3D:2.60.40.10&Pfam:PF07686&PROSITE_profiles:PS50835&PANTHER:PTHR44793&SMART:SM00406&SMART:SM00409&Superfamily:SSF48726||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000478517|retained_intron|||||||||||1245|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344595|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:167,4:0.026:171:76,2:65,1:146,3:111,56,3,1
chr1	1356892	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=3;ECNT=1;GERMQ=32;MBQ=0,37;MFRL=0,178;MMQ=60,60;MPOS=2;POPAF=7.3;ROQ=10;TLOD=7.45;CSQ=A|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000309212|protein_coding||1/9|ENST00000309212.11:c.50-188C>T|||||||||-1||SNV|HGNC|HGNC:7542|YES|NM_032348.4||1|P2|CCDS24.1|ENSP00000307887|Q9BRK3.164||UPI000003ED26|Q9BRK3-1||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000342753|protein_coding||1/8|ENST00000342753.8:c.50-188C>T|||||||||-1||SNV|HGNC|HGNC:7542||||1||CCDS59950.1|ENSP00000344998|Q9BRK3.164||UPI00001A7404|Q9BRK3-4||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000445648|protein_coding||1/9|ENST00000445648.5:c.50-188C>T|||||||||-1||SNV|HGNC|HGNC:7542||||2|A2|CCDS59951.1|ENSP00000399229|Q9BRK3.164||UPI0000470B85|Q9BRK3-2||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000460473|retained_intron|||||||||||1380|-1||SNV|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000464351|retained_intron|||||||||||1380|-1||SNV|HGNC|HGNC:7542||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000473097|retained_intron|||||||||||2418|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000474033|retained_intron|||||||||||2628|-1||SNV|HGNC|HGNC:7542||||1|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000476718|retained_intron|||||||||||1876|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding||1/9|ENST00000477278.3:c.23-188C>T|||||||||-1||SNV|HGNC|HGNC:7542||||5|A2|CCDS59952.1|ENSP00000436135|Q9BRK3.164||UPI000013E183|Q9BRK3-3||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000478517|retained_intron|||||||||||2645|-1||SNV|HGNC|HGNC:7542||||3|||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344595|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,2:0.764:2:0,2:0,0:0,2:0,0,0,2
chr1	1364790	.	T	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,96;MMQ=60,40;MPOS=4;POPAF=7.3;ROQ=20;TLOD=3.88;CSQ=C|upstream_gene_variant|MODIFIER|MXRA8|ENSG00000162576|Transcript|ENST00000477278|protein_coding||||||||||rs1273359571|3013|-1||SNV|HGNC|HGNC:7542||||5|A2|CCDS59952.1|ENSP00000436135|Q9BRK3.164||UPI000013E183|Q9BRK3-3||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1373781	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=138,26|3,2;DP=191;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=123,135;MMQ=60,60;MPOS=36;POPAF=4.61;ROQ=4;TLOD=6.1;CSQ=T|3_prime_UTR_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000321751|protein_coding|4/4||ENST00000321751.9:c.*20G>A||749|||||rs780252686||-1||SNV|HGNC|HGNC:24114||||2|P1|CCDS25.1|ENSP00000319778|Q9NWT8.149||UPI00000709CC||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|3_prime_UTR_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000338338|protein_coding|4/4||ENST00000338338.10:c.*20G>A||708|||||rs780252686||-1||SNV|HGNC|HGNC:24114|YES|NM_017900.3||1|P1|CCDS25.1|ENSP00000340656|Q9NWT8.149||UPI00000709CC||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|3_prime_UTR_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000338370|protein_coding|3/3||ENST00000338370.7:c.*20G>A||1021|||||rs780252686||-1||SNV|HGNC|HGNC:24114||||1|P1|CCDS25.1|ENSP00000342676|Q9NWT8.149||UPI00000709CC||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|3_prime_UTR_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000378853|protein_coding|4/4||ENST00000378853.3:c.*20G>A||831|||||rs780252686||-1||SNV|HGNC|HGNC:24114||||2|P1|CCDS25.1|ENSP00000368130|Q9NWT8.149||UPI00000709CC||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|upstream_gene_variant|MODIFIER|NDUFB4P8|ENSG00000223663|Transcript|ENST00000435351|processed_pseudogene||||||||||rs780252686|4885|1||SNV|HGNC|HGNC:45256|YES|||||||||||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|downstream_gene_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000489799|processed_transcript||||||||||rs780252686|463|-1||SNV|HGNC|HGNC:24114||||1||||||||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|downstream_gene_variant|MODIFIER|AURKAIP1|ENSG00000175756|Transcript|ENST00000496905|processed_transcript||||||||||rs780252686|657|-1||SNV|HGNC|HGNC:24114||||2||||||||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000184|promoter||||||||||rs780252686||||SNV||||||||||||||||||||||||||||0.0002196|0|0|0|0|0|0|0|0.001686|0.001686|gnomAD_SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:164,5:0.026:169:55,2:88,1:147,3:138,26,3,2
chr1	1392922	.	A	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=6,25|1,3;DP=35;ECNT=1;GERMQ=80;MBQ=37,23;MFRL=165,136;MMQ=60,60;MPOS=26;POPAF=7.3;ROQ=6;TLOD=7.02;CSQ=G|intron_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000400809|protein_coding||5/10|ENST00000400809.8:c.659+474T>C|||||||||-1||SNV|HGNC|HGNC:20570|YES|NM_030937.6||1|P1|CCDS30557.1|ENSP00000383611|Q96S94.163||UPI00000713F5|Q96S94-1||||||||||||||||||||||||||||||||||,G|intron_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000408918|protein_coding||5/5|ENST00000408918.8:c.660-119T>C|||||||||-1||SNV|HGNC|HGNC:20570||||1||CCDS30558.1|ENSP00000386158|Q96S94.163||UPI000022B1CA|Q96S94-5||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000418865|retained_intron|||||||||||397|-1||SNV|HGNC|HGNC:20570||||1|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000425598|nonsense_mediated_decay|||||||||||522|-1||SNV|HGNC|HGNC:20570||||5|||ENSP00000392899||C9J148.88|UPI00006C0120|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000463260|retained_intron|||||||||||4209|-1||SNV|HGNC|HGNC:20570||||1|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000463895|retained_intron|||||||||||2263|-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000469113|processed_transcript|||||||||||206|-1||SNV|HGNC|HGNC:20570||||3|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000471930|processed_transcript||3/4|ENST00000471930.5:n.321-119T>C|||||||||-1||SNV|HGNC|HGNC:20570||||5|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000473872|retained_intron|||||||||||158|-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000480479|retained_intron|||||||||||1826|-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000480646|retained_intron|||||||||||1918|-1||SNV|HGNC|HGNC:20570||||3|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000481223|nonsense_mediated_decay||5/11|ENST00000481223.6:c.660-119T>C|||||||||-1||SNV|HGNC|HGNC:20570||||2|||ENSP00000423734|Q96S94.163||UPI00006C0124|Q96S94-4||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000482365|retained_intron|||||||||||1168|-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000482621|nonsense_mediated_decay||3/9|ENST00000482621.5:c.*143-119T>C|||||||||-1|cds_start_NF|SNV|HGNC|HGNC:20570||||2|||ENSP00000462056||J3KRL1.36|UPI000268AE27|||||||||||||||||||||||||||||||||||,G|intron_variant&NMD_transcript_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000488340|nonsense_mediated_decay||5/11|ENST00000488340.5:c.660-119T>C|||||||||-1||SNV|HGNC|HGNC:20570||||2|||ENSP00000424647|Q96S94.163||UPI0000070AEB|Q96S94-2||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000492998|retained_intron|||||||||||2022|-1||SNV|HGNC|HGNC:20570||||3|||||||||||||||||||||||||||||||||||||||||,G|intron_variant&non_coding_transcript_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000496007|retained_intron||5/12|ENST00000496007.5:n.663-119T>C|||||||||-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||,G|downstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000497013|protein_coding|||||||||||2515|-1|cds_end_NF|SNV|HGNC|HGNC:20570||||2|||ENSP00000464685||J3QSH2.60|UPI0003F47EDC|||||||||||||||||||||||||||||||||||,G|upstream_gene_variant|MODIFIER|CCNL2|ENSG00000221978|Transcript|ENST00000505849|processed_transcript|||||||||||1273|-1||SNV|HGNC|HGNC:20570||||2|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:31,4:0.133:35:17,3:8,0:25,3:6,25,1,3
chr1	1407259	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=29,176|2,8;DP=221;ECNT=2;GERMQ=93;MBQ=37,29;MFRL=146,168;MMQ=60,60;MPOS=15;POPAF=7.3;ROQ=50;TLOD=16.51;CSQ=A|5_prime_UTR_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000344843|protein_coding|1/4||ENST00000344843.12:c.-42G>T||35|||||||-1||SNV|HGNC|HGNC:14478|YES|NM_017971.4||1|P1|CCDS26.1|ENSP00000341082|Q9BYC9.167||UPI000006F0A8|Q9BYC9-1||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000477686|processed_transcript|||||||||||24|-1||SNV|HGNC|HGNC:14478||||3|||||||||||||||||||||||||||||||||||||||||,A|5_prime_UTR_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000482352|protein_coding|1/3||ENST00000482352.1:c.-42G>T||32|||||||-1||SNV|HGNC|HGNC:14478||||2|||ENSP00000460924|Q9BYC9.167||UPI00019151C3|Q9BYC9-2||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000487659|retained_intron|1/3||ENST00000487659.1:n.10G>T||10|||||||-1||SNV|HGNC|HGNC:14478||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000492508|protein_coding|||||||||||261|-1|cds_start_NF|SNV|HGNC|HGNC:14478||||2|||ENSP00000459994||I3L2X1.49|UPI00025A2C10|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MRPL20|ENSG00000242485|Transcript|ENST00000493287|processed_transcript|||||||||||952|-1||SNV|HGNC|HGNC:14478||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|RN7SL657P|ENSG00000264293|Transcript|ENST00000582431|misc_RNA|||||||||||1507|-1||SNV|HGNC|HGNC:46673|YES||||||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|MRPL20-DT|ENSG00000272455|Transcript|ENST00000607307|lncRNA|||||||||||1837|1||SNV|HGNC|HGNC:54814|YES||||||||||||||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000188|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189916435|||||||||||||1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0564|18|Y|0.009|TEAD4::MAX,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00159249655|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0427|4|Y|-0.089|NRF1,A|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189221670|||||||||||||-1||SNV|||||||||||||||||||||||||||||||||||||||||||ENSPFM0403|19|Y|-0.074|MYBL1::MAX	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:205,10:0.044:215:87,4:61,3:178,8:29,176,2,8
chr1	1423537	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=2;ECNT=1;GERMQ=32;MBQ=0,20;MFRL=0,60;MMQ=60,54;MPOS=24;POPAF=7.3;ROQ=9;TLOD=4.62;CSQ=A|upstream_gene_variant|MODIFIER|TMEM88B|ENSG00000205116|Transcript|ENST00000378821|protein_coding||||||||||rs1376899091|2334|1||SNV|HGNC|HGNC:37099|YES|NM_001146685.2||2|P1|CCDS57964.1|ENSP00000455099|A6NKF7.83||UPI0000D61E0D|||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ANKRD65|ENSG00000235098|Transcript|ENST00000427211|protein_coding||||||||||rs1376899091|1768|-1||SNV|HGNC|HGNC:42950||||1||CCDS57962.1|ENSP00000428419|E5RJM6.76||UPI000015FF0A|E5RJM6-2||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER||ENSG00000225905|Transcript|ENST00000428932|lncRNA||||||||||rs1376899091|846|1||SNV|||YES|||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ANKRD65|ENSG00000235098|Transcript|ENST00000442470|protein_coding||||||||||rs1376899091|2277|-1||SNV|HGNC|HGNC:42950||||2||CCDS57962.1|ENSP00000428201|E5RJM6.76||UPI000015FF0A|E5RJM6-2||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ANKRD65|ENSG00000235098|Transcript|ENST00000454272|protein_coding||||||||||rs1376899091|2446|-1||SNV|HGNC|HGNC:42950||||5|P1|CCDS55558.1|ENSP00000482314|E5RJM6.76||UPI000058F1BA|E5RJM6-1||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ANKRD65|ENSG00000235098|Transcript|ENST00000520296|protein_coding||||||||||rs1376899091|2093|-1||SNV|HGNC|HGNC:42950||||1||CCDS57963.1|ENSP00000429035|E5RJM6.76||UPI0001E8F3CB|E5RJM6-3||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ANKRD65|ENSG00000235098|Transcript|ENST00000537107|protein_coding||||||||||rs1376899091|2261|-1||SNV|HGNC|HGNC:42950|YES|NM_001145210.3||5|P1|CCDS55558.1|ENSP00000445688|E5RJM6.76||UPI000058F1BA|E5RJM6-1||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,2:0.667:2:0,0:0,1:0,1:0,0,1,1
chr1	1437558	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=3,20|1,3;DP=34;ECNT=2;GERMQ=60;MBQ=37,29;MFRL=167,167;MMQ=60,60;MPOS=17;POPAF=7.3;ROQ=15;TLOD=8.5;CSQ=A|intron_variant|MODIFIER|VWA1|ENSG00000179403|Transcript|ENST00000338660|protein_coding||2/2|ENST00000338660.5:c.*41+74G>A|||||||||1||SNV|HGNC|HGNC:30910||||2||CCDS28.2|ENSP00000423404|Q6PCB0.151||UPI0001BC0386|Q6PCB0-3|1|||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01770|ENSG00000225285|Transcript|ENST00000417917|lncRNA|||||||||||3038|-1||SNV|HGNC|HGNC:52560||||2|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01770|ENSG00000225285|Transcript|ENST00000430109|lncRNA|||||||||||2985|-1||SNV|HGNC|HGNC:52560|YES|||3|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|LINC01770|ENSG00000225285|Transcript|ENST00000454562|lncRNA|||||||||||3070|-1||SNV|HGNC|HGNC:52560||||3|||||||||||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|VWA1|ENSG00000179403|Transcript|ENST00000471398|protein_coding|||||||||||381|1|cds_end_NF|SNV|HGNC|HGNC:30910||||3|||ENSP00000464343||J3QRR0.53|UPI000268AE2B||1|||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|VWA1|ENSG00000179403|Transcript|ENST00000476993|protein_coding||2/2|ENST00000476993.2:c.631+74G>A|||||||||1||SNV|HGNC|HGNC:30910|YES|NM_022834.5||1|P1|CCDS27.1|ENSP00000417185|Q6PCB0.151||UPI00001D9616|Q6PCB0-1|1|||||||||||||||||||||||||||||||||,A|downstream_gene_variant|MODIFIER|VWA1|ENSG00000179403|Transcript|ENST00000495558|protein_coding|||||||||||99|1|cds_end_NF|SNV|HGNC|HGNC:30910||||2|||ENSP00000463643||J3QLP3.50|UPI000268AE2A||1|||||||||||||||||||||||||||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000000192|promoter||||||||||||||SNV|||||||||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:23,4:0.151:27:12,2:9,1:21,3:3,20,1,3
chr1	1452460	.	G	GCCCCTCA	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=36,113|0,4;DP=163;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=135,217;MMQ=40,40;MPOS=18;POPAF=7.3;ROQ=93;TLOD=8.56;CSQ=CCCCTCA|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||3/11|ENST00000378785.7:c.222+26_222+27insCCCCTCA|||||||||1||insertion|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,CCCCTCA|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||4/5|ENST00000475091.2:c.222+26_222+27insCCCCTCA|||||||||1|cds_end_NF|insertion|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:149,4:0.034:153:35,1:43,3:133,4:0|1:1452460_G_GCCCCTCA:1452460:36,113,0,4
chr1	1452461	.	G	GCCACCTGC	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=36,113|0,4;DP=161;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=135,217;MMQ=40,40;MPOS=10;POPAF=7.3;ROQ=93;TLOD=8.57;CSQ=CCACCTGC|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||3/11|ENST00000378785.7:c.222+28_222+29insCACCTGCC|||||||||1||insertion|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,CCACCTGC|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||4/5|ENST00000475091.2:c.222+28_222+29insCACCTGCC|||||||||1|cds_end_NF|insertion|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:149,4:0.034:153:35,1:43,3:133,4:0|1:1452460_G_GCCCCTCA:1452460:36,113,0,4
chr1	1455403	.	GGTGGCTGTTCC	G	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=72,19|6,1;DP=123;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=119,159;MMQ=54,60;MPOS=19;POPAF=7.3;ROQ=93;TLOD=21.15;CSQ=-|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||4/11|ENST00000378785.7:c.379-48_379-38del|||||||||1||deletion|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,-|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||4/5|ENST00000475091.2:c.223-48_223-38del|||||||||1|cds_end_NF|deletion|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:91,7:0.084:98:28,0:27,6:79,6:72,19,6,1
chr1	1455662	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=9,9|2,3;DP=24;ECNT=1;GERMQ=42;MBQ=37,20;MFRL=195,264;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=3;TLOD=10.01;CSQ=A|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||5/11|ENST00000378785.7:c.439-129G>A|||||||||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,A|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||5/5|ENST00000475091.2:c.283-129G>A|||||||||1|cds_end_NF|SNV|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C|||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:18,5:0.19:23:7,0:9,3:16,3:9,9,2,3
chr1	1457166	.	C	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=55,101|1,5;DP=181;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=126,167;MMQ=52,45;MPOS=9;POPAF=7.3;ROQ=6;TLOD=10.61;CSQ=A|synonymous_variant|LOW|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding|8/12||ENST00000378785.7:c.727C>A|ENSP00000368062.2:p.Arg243%3D|1722|727|243|R|Cgg/Agg|rs536232078&COSV66482513||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||Gene3D:3.40.50.300&Pfam:PF00004&PANTHER:PTHR23075&PANTHER:PTHR23075:SF2&SMART:SM00382&Superfamily:SSF52540&CDD:cd00009|||||||||||||||||||||||0&1|0&1||||||,A|downstream_gene_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||||||||||rs536232078&COSV66482513|1264|1|cds_end_NF|SNV|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C||||||||||||||||||||||||||||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	0|1:156,6:0.044:162:59,5:57,0:127,5:0|1:1457166_C_A:1457166:55,101,1,5
chr1	1457167	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=55,106|1,5;DP=179;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=126,138;MMQ=52,53;MPOS=3;POPAF=3.65;ROQ=16;TLOD=14.33;CSQ=A|missense_variant|MODERATE|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding|8/12||ENST00000378785.7:c.728G>A|ENSP00000368062.2:p.Arg243Gln|1723|728|243|R/Q|cGg/cAg|rs375870663&COSV101112628&COSV66482805||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||tolerated(0.1)|benign(0.358)|Gene3D:3.40.50.300&Pfam:PF00004&PANTHER:PTHR23075&PANTHER:PTHR23075:SF2&SMART:SM00382&Superfamily:SSF52540&CDD:cd00009|||||||||0|0.0003143|0.0001675|6.176e-05|8.674e-05|0|0|0|0.000265|0.0001632|0.0002287|0.0003143|EA||0&1&1|0&1&1||||||,A|downstream_gene_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000475091|protein_coding||||||||||rs375870663&COSV101112628&COSV66482805|1265|1|cds_end_NF|SNV|HGNC|HGNC:32151||||5|||ENSP00000464661||J3QSF3.49|UPI000268AE2C||||||||||||||0|0.0003143|0.0001675|6.176e-05|8.674e-05|0|0|0|0.000265|0.0001632|0.0002287|0.0003143|EA||0&1&1|0&1&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:PGT:PID:PS:SB	1|0:161,6:0.043:167:64,2:55,3:132,5:1|0:1457166_C_A:1457166:55,106,1,5
chr1	1460987	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=12,65|2,2;DP=82;ECNT=1;GERMQ=93;MBQ=37,20;MFRL=165,143;MMQ=60,60;MPOS=57;POPAF=4.13;ROQ=8;TLOD=4.67;CSQ=T|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||10/11|ENST00000378785.7:c.980+70C>T|||||||rs947048992||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000484537|retained_intron||||||||||rs947048992|1496|1||SNV|HGNC|HGNC:32151||||1|||||||||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:77,4:0.043:81:32,1:32,1:65,2:12,65,2,2
chr1	1462601	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=155,87|4,1;DP=255;ECNT=1;GERMQ=93;MBQ=37,37;MFRL=125,110;MMQ=56,53;MPOS=20;POPAF=4.61;ROQ=3;TLOD=6.82;CSQ=T|missense_variant&splice_region_variant|MODERATE|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding|11/12||ENST00000378785.7:c.982C>T|ENSP00000368062.2:p.Arg328Cys|1977|982|328|R/C|Cgt/Tgt|rs535863359&COSV66482433||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||deleterious(0)|possibly_damaging(0.88)|PANTHER:PTHR23075&PANTHER:PTHR23075:SF2&Superfamily:SSF52540|||0.0002|0.0008|0|0|0|0|||8.624e-05|7.352e-05|0|0|0.001038|0|1.008e-05|0|0|0.001038|gnomAD_EAS||0&1|0&1||||||,T|non_coding_transcript_exon_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000484537|retained_intron|1/2||ENST00000484537.2:n.119C>T||119|||||rs535863359&COSV66482433||1||SNV|HGNC|HGNC:32151||||1||||||||||||||0.0002|0.0008|0|0|0|0|||8.624e-05|7.352e-05|0|0|0.001038|0|1.008e-05|0|0|0.001038|gnomAD_EAS||0&1|0&1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344642|promoter||||||||||rs535863359&COSV66482433||||SNV||||||||||||||||||||0.0002|0.0008|0|0|0|0|||8.624e-05|7.352e-05|0|0|0.001038|0|1.008e-05|0|0|0.001038|gnomAD_EAS||0&1|0&1||||||,T|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344644|CTCF_binding_site||||||||||rs535863359&COSV66482433||||SNV||||||||||||||||||||0.0002|0.0008|0|0|0|0|||8.624e-05|7.352e-05|0|0|0.001038|0|1.008e-05|0|0|0.001038|gnomAD_EAS||0&1|0&1||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:242,5:0.024:247:99,1:103,3:204,4:155,87,4,1
chr1	1462875	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,1|1,1;DP=3;ECNT=1;GERMQ=2;MBQ=37,20;MFRL=268,215;MMQ=60,60;MPOS=12;POPAF=4.61;ROQ=5;TLOD=4.17;CSQ=A|intron_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||11/11|ENST00000378785.7:c.1089+167G>A|||||||rs558173439||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0||||||||0.0002|0|0|0|0|0.001||||||||||||0.001|SAS|||||||||,A|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000484537|retained_intron||1/1|ENST00000484537.2:n.226+167G>A|||||||rs558173439||1||SNV|HGNC|HGNC:32151||||1||||||||||||||0.0002|0|0|0|0|0.001||||||||||||0.001|SAS|||||||||,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000344642|promoter||||||||||rs558173439||||SNV||||||||||||||||||||0.0002|0|0|0|0|0.001||||||||||||0.001|SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:1,2:0.5:3:1,1:0,0:1,1:0,1,1,1
chr1	1468566	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=13,87|1,5;DP=108;ECNT=2;GERMQ=93;MBQ=37,31;MFRL=135,136;MMQ=40,40;MPOS=1;POPAF=4.61;ROQ=19;TLOD=10.4;CSQ=A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||||||||||rs754436632|3218|1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5||||||||||||||||1.433e-05|0|0|0|7.571e-05|0|0|0|7.535e-05|7.571e-05|gnomAD_EAS|||||||||,A|3_prime_UTR_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding|12/12||ENST00000378785.7:c.*36G>A||2267|||||rs754436632||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0||||||||||||||||1.433e-05|0|0|0|7.571e-05|0|0|0|7.535e-05|7.571e-05|gnomAD_EAS|||||||||,A|non_coding_transcript_exon_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000484537|retained_intron|2/2||ENST00000484537.2:n.409G>A||409|||||rs754436632||1||SNV|HGNC|HGNC:32151||||1||||||||||||||||||||||1.433e-05|0|0|0|7.571e-05|0|0|0|7.535e-05|7.571e-05|gnomAD_EAS|||||||||,A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||||||||||rs754436632|3199|1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1|||||||||||||||1.433e-05|0|0|0|7.571e-05|0|0|0|7.535e-05|7.571e-05|gnomAD_EAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:100,6:0.063:106:38,3:50,2:88,5:13,87,1,5
chr1	1468593	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=6,39|0,3;DP=73;ECNT=2;GERMQ=93;MBQ=37,37;MFRL=151,160;MMQ=40,40;MPOS=20;POPAF=7.3;ROQ=9;TLOD=6.71;CSQ=A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||||||||||rs955967059|3191|1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5|||||||||||||||||||||||||||||||||||,A|3_prime_UTR_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding|12/12||ENST00000378785.7:c.*63G>A||2294|||||rs955967059||1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,A|non_coding_transcript_exon_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000484537|retained_intron|2/2||ENST00000484537.2:n.436G>A||436|||||rs955967059||1||SNV|HGNC|HGNC:32151||||1|||||||||||||||||||||||||||||||||||||||||,A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||||||||||rs955967059|3172|1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:45,3:0.086:48:20,1:20,2:40,3:6,39,0,3
chr1	1474479	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|0,0;DP=1;ECNT=1;GERMQ=31;MBQ=0,37;MFRL=0,150;MMQ=60,60;MPOS=19;POPAF=7.3;ROQ=7;TLOD=3.88;CSQ=T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||1/13|ENST00000308647.8:c.205+2390C>T|||||||rs1270383449||1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000378736|processed_transcript||||||||||rs1270383449|4570|1||SNV|HGNC|HGNC:24007||||5|||||||||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ATAD3C|ENSG00000215915|Transcript|ENST00000378785|protein_coding||||||||||rs1270383449|4316|1||SNV|HGNC|HGNC:32151|YES|NM_001039211.3||2|P1|CCDS44039.1|ENSP00000368062|Q5T2N8.139||UPI00001619C0|||||||||||||||||||||||||||||||||||,T|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000472194|retained_intron||||||||||rs1270383449|3547|1||SNV|HGNC|HGNC:24007||||1|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||1/15|ENST00000673477.1:c.205+2390C>T|||||||rs1270383449||1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,1:0.667:1:0,0:0,1:0,1:0,0,1,0
chr1	1477486	.	G	A	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=4,13|0,3;DP=20;ECNT=1;GERMQ=21;MBQ=37,37;MFRL=190,192;MMQ=60,60;MPOS=22;POPAF=4.13;ROQ=14;TLOD=8.35;CSQ=A|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||2/13|ENST00000308647.8:c.282+136G>A|||||||rs534615999||1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5||||||||0.0014|0|0.0014|0|0|0.0061||||||||||||0.0061|SAS|||||||||,A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000378736|processed_transcript||||||||||rs534615999|1563|1||SNV|HGNC|HGNC:24007||||5||||||||||||||0.0014|0|0.0014|0|0|0.0061||||||||||||0.0061|SAS|||||||||,A|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000472194|retained_intron||||||||||rs534615999|540|1||SNV|HGNC|HGNC:24007||||1||||||||||||||0.0014|0|0.0014|0|0|0.0061||||||||||||0.0061|SAS|||||||||,A|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||2/15|ENST00000673477.1:c.282+136G>A|||||||rs534615999||1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1|||||||0.0014|0|0.0014|0|0|0.0061||||||||||||0.0061|SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:17,3:0.201:20:9,1:5,2:15,3:4,13,0,3
chr1	1482715	.	T	C	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=1,38|0,2;DP=41;ECNT=1;GERMQ=90;MBQ=37,37;MFRL=166,241;MMQ=57,60;MPOS=18;POPAF=4.31;ROQ=3;TLOD=3.85;CSQ=C|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||5/13|ENST00000308647.8:c.432+101T>C|||||||rs756863050||1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5||||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||,C|downstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000378736|processed_transcript||||||||||rs756863050|53|1||SNV|HGNC|HGNC:24007||||5||||||||||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||,C|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000472194|retained_intron||5/13|ENST00000472194.6:n.1086+101T>C|||||||rs756863050||1||SNV|HGNC|HGNC:24007||||1||||||||||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||,C|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000474481|retained_intron||||||||||rs756863050|1854|1||SNV|HGNC|HGNC:24007||||2||||||||||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||,C|upstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000485748|retained_intron||||||||||rs756863050|770|1||SNV|HGNC|HGNC:24007||||2||||||||||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||,C|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||7/15|ENST00000673477.1:c.750+101T>C|||||||rs756863050||1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1|||||||||||||||8.773e-06|0.000142|0|0|0|0|0|0|0|0.000142|gnomAD_AFR|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:39,2:0.071:41:23,2:15,0:38,2:1,38,0,2
chr1	1486686	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=0,0|2,1;DP=3;ECNT=1;GERMQ=35;MBQ=0,20;MFRL=0,184;MMQ=60,44;MPOS=53;POPAF=7.3;ROQ=8;TLOD=7.42;CSQ=T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||9/13|ENST00000308647.8:c.*2+18C>T|||||||||1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5|||||||||||||||||||||||||||||||||||,T|downstream_gene_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000378736|processed_transcript|||||||||||4024|1||SNV|HGNC|HGNC:24007||||5|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000472194|retained_intron||9/13|ENST00000472194.6:n.1550+18C>T|||||||||1||SNV|HGNC|HGNC:24007||||1|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000474481|retained_intron||3/4|ENST00000474481.1:n.1182+18C>T|||||||||1||SNV|HGNC|HGNC:24007||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000485748|retained_intron||4/9|ENST00000485748.5:n.1995+18C>T|||||||||1||SNV|HGNC|HGNC:24007||||2|||||||||||||||||||||||||||||||||||||||||,T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||11/15|ENST00000673477.1:c.1214+18C>T|||||||||1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1||||||||||||||||||||||||||||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:0,3:0.75:3:0,0:0,2:0,2:0,0,2,1
chr1	1489325	.	C	T	.	PASS	AS_FilterStatus=SITE;AS_SB_TABLE=17,128|1,2;DP=158;ECNT=2;GERMQ=93;MBQ=37,20;MFRL=135,139;MMQ=54,60;MPOS=51;POPAF=7.3;ROQ=7;TLOD=3.01;CSQ=T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000308647|protein_coding||11/13|ENST00000308647.8:c.*125+51C>T|||||||rs746865760||1||SNV|HGNC|HGNC:24007||||1|||ENSP00000311766||A0A5K1VW56.8|UPI001235A3B5||||||||||||||||1.605e-05|0|0|0|0|0|2.677e-05|0|3.277e-05|3.277e-05|gnomAD_SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000472194|retained_intron||11/13|ENST00000472194.6:n.1673+51C>T|||||||rs746865760||1||SNV|HGNC|HGNC:24007||||1||||||||||||||||||||||1.605e-05|0|0|0|0|0|2.677e-05|0|3.277e-05|3.277e-05|gnomAD_SAS|||||||||,T|non_coding_transcript_exon_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000474481|retained_intron|4/5||ENST00000474481.1:n.1304C>T||1304|||||rs746865760||1||SNV|HGNC|HGNC:24007||||2||||||||||||||||||||||1.605e-05|0|0|0|0|0|2.677e-05|0|3.277e-05|3.277e-05|gnomAD_SAS|||||||||,T|intron_variant&non_coding_transcript_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000485748|retained_intron||6/9|ENST00000485748.5:n.2118+51C>T|||||||rs746865760||1||SNV|HGNC|HGNC:24007||||2||||||||||||||||||||||1.605e-05|0|0|0|0|0|2.677e-05|0|3.277e-05|3.277e-05|gnomAD_SAS|||||||||,T|intron_variant|MODIFIER|ATAD3B|ENSG00000160072|Transcript|ENST00000673477|protein_coding||13/15|ENST00000673477.1:c.1337+51C>T|||||||rs746865760||1||SNV|HGNC|HGNC:24007|YES|NM_031921.6|||P1|CCDS30.1|ENSP00000500094|Q5T9A4.153||UPI000013E044|Q5T9A4-1|||||||||||||||1.605e-05|0|0|0|0|0|2.677e-05|0|3.277e-05|3.277e-05|gnomAD_SAS|||||||||	GT:AD:AF:DP:F1R2:F2R1:FAD:SB	0/1:145,3:0.022:148:59,1:66,1:130,2:17,128,1,2