contig	pos	id	ref	alt	qual	filter	info_AS_FilterStatus	info_AS_SB_TABLE	info_AS_UNIQ_ALT_READ_COUNT	info_CONTQ	info_DP	info_ECNT	info_GERMQ	info_MBQ	info_MFRL	info_MMQ	info_MPOS	info_NALOD	info_NCount	info_NLOD	info_OCM	info_PON	info_POPAF	info_ROQ	info_RPA	info_RU	info_SEQQ	info_STR	info_STRANDQ	info_STRQ	info_TLOD	vep_Allele	vep_Consequence	vep_IMPACT	vep_SYMBOL	vep_Gene	vep_Feature_type	vep_Feature	vep_BIOTYPE	vep_EXON	vep_INTRON	vep_HGVSc	vep_HGVSp	vep_cDNA_position	vep_CDS_position	vep_Protein_position	vep_Amino_acids	vep_Codons	vep_Existing_variation	vep_DISTANCE	vep_STRAND	vep_FLAGS	vep_VARIANT_CLASS	vep_SYMBOL_SOURCE	vep_HGNC_ID	vep_CANONICAL	vep_MANE_SELECT	vep_MANE_PLUS_CLINICAL	vep_TSL	vep_APPRIS	vep_CCDS	vep_ENSP	vep_SWISSPROT	vep_TREMBL	vep_UNIPARC	vep_UNIPROT_ISOFORM	vep_GENE_PHENO	vep_SIFT	vep_PolyPhen	vep_DOMAINS	vep_miRNA	vep_HGVS_OFFSET	vep_AF	vep_AFR_AF	vep_AMR_AF	vep_EAS_AF	vep_EUR_AF	vep_SAS_AF	vep_AA_AF	vep_EA_AF	vep_gnomAD_AF	vep_gnomAD_AFR_AF	vep_gnomAD_AMR_AF	vep_gnomAD_ASJ_AF	vep_gnomAD_EAS_AF	vep_gnomAD_FIN_AF	vep_gnomAD_NFE_AF	vep_gnomAD_OTH_AF	vep_gnomAD_SAS_AF	vep_MAX_AF	vep_MAX_AF_POPS	vep_CLIN_SIG	vep_SOMATIC	vep_PHENO	vep_PUBMED	vep_MOTIF_NAME	vep_MOTIF_POS	vep_HIGH_INF_POS	vep_MOTIF_SCORE_CHANGE	vep_TRANSCRIPTION_FACTORS	CSQ_other_transcripts	AD	AF	DP	F1R2	F2R1	FAD	GQ	GT	PGT	PID	PL	PS	SB	sample
chr1	13421		A	AAATGTGATCTCTCTCGGGG	NA	PASS	SITE	3,9|0,3	NA	NA	17	2	7	29,20	174,107	34,44	20	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	9.87	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||||||||||||||||||||||||||||||||||||||||||||||||	12,3	0.282	15	4,2	2,0	10,3	NA	1|0	1|0	13417_C_CGAGA	NA	13417	3,9,0,3	pakistan1_PS-9941-44_tumour
chr1	647483		A	C	NA	PASS	SITE	0,0|0,0	NA	NA	2	1	32	0,20	0,82	60,37	13	NA	NA	NA	NA	NA	7.3	33	NA	NA	NA	NA	NA	NA	4.61	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||||||||||||||||||||||||||||||||||||||||||||||||	0,2	0.667	2	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,1	pakistan1_PS-9941-44_tumour
chr1	674844		A	T	NA	PASS	SITE	35,9|3,2	NA	NA	53	1	93	37,20	128,166	50,60	53	NA	NA	NA	NA	NA	7.3	3	NA	NA	NA	NA	NA	NA	8.26	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||||||||||||||||||||||||||||||||||||||||||||||||	44,5	0.099	49	21,0	13,3	35,3	NA	0/1	NA	NA	NA	NA	35,9,3,2	pakistan1_PS-9941-44_tumour
chr1	778107		T	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,100	60,39	8	NA	NA	NA	NA	NA	7.3	28	NA	NA	NA	NA	NA	NA	3.88	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|	0,1	0.667	1	0,1	0,0	0,1	NA	0/1	NA	NA	NA	NA	0,0,0,1	pakistan1_PS-9941-44_tumour
chr1	781965		A	T	NA	PASS	SITE	55,25|3,1	NA	NA	86	1	93	37,29	115,154	53,44	27	NA	NA	NA	NA	NA	7.3	2	NA	NA	NA	NA	NA	NA	4.69	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||||||||||||||||||||||||||||||||||||||||||||||||	80,4	0.058	84	34,0	27,3	64,3	NA	0/1	NA	NA	NA	NA	55,25,3,1	pakistan1_PS-9941-44_tumour
chr1	805966		C	T	NA	PASS	SITE	4,4|1,1	NA	NA	10	1	11	20,20	157,160	47,47	31	NA	NA	NA	NA	NA	4.61	3	NA	NA	NA	NA	NA	NA	3.47	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||||||||||||||||||||||||||||||||||||||||||||||	8,2	0.286	10	2,1	2,0	4,1	NA	0/1	NA	NA	NA	NA	4,4,1,1	pakistan1_PS-9941-44_tumour
chr1	874082		C	T	NA	PASS	SITE	37,10|7,0	NA	NA	61	1	93	37,37	195,280	60,60	6	NA	NA	NA	NA	NA	7.3	22	NA	NA	NA	NA	NA	NA	16.57	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|||||||||||||||||||||||||||||||||||||||||||||	47,7	0.148	54	25,4	17,2	42,7	NA	0/1	NA	NA	NA	NA	37,10,7,0	pakistan1_PS-9941-44_tumour
chr1	874370		AGG	A	NA	PASS	SITE	30,69|2,4	NA	NA	113	2	93	37,20	114,164	60,60	22	NA	NA	NA	NA	NA	7.3	93	6,4	G	NA	true	NA	93	9.37	-	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|||||||||||||||||||||||||||||||||||||||||||||	99,6	0.058	105	18,4	27,0	80,4	NA	0/1	NA	NA	NA	NA	30,69,2,4	pakistan1_PS-9941-44_tumour
chr1	898145		C	T	NA	PASS	SITE	25,5|3,0	NA	NA	39	1	56	37,37	118,103	60,50	3	NA	NA	NA	NA	NA	4.31	12	NA	NA	NA	NA	NA	NA	7.46	T	regulatory_region_variant	MODIFIER			RegulatoryFeature	ENSR00000918361	promoter_flanking_region										rs1049059485				SNV																																																T|intergenic_variant|MODIFIER|||||||||||||||rs1049059485||||SNV||||||||||||||||||||||||||||||||||||||||||||||||	30,3	0.127	33	14,1	12,2	26,3	NA	0/1	NA	NA	NA	NA	25,5,3,0	pakistan1_PS-9941-44_tumour
chr1	918937		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,143	60,60	26	NA	NA	NA	NA	NA	7.3	10	NA	NA	NA	NA	NA	NA	3.88	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||||||||||	0,1	0.667	1	0,1	0,0	0,1	NA	0/1	NA	NA	NA	NA	0,0,0,1	pakistan1_PS-9941-44_tumour
chr1	924751		C	A	NA	PASS	SITE	90,93|1,3	NA	NA	189	2	93	37,37	128,123	60,60	6	NA	NA	NA	NA	NA	7.3	25	NA	NA	NA	NA	NA	NA	9.94	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||||||||||||||||||||||||||||||||||||||||||||||||	183,4	0.024	187	67,1	74,2	159,3	NA	0|1	0|1	924751_C_A	NA	924751	90,93,1,3	pakistan1_PS-9941-44_tumour
chr1	924754		T	G	NA	PASS	SITE	95,94|1,3	NA	NA	195	2	93	37,37	128,123	60,60	3	NA	NA	NA	NA	NA	7.3	31	NA	NA	NA	NA	NA	NA	9.89	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||||||||||||||||||||||||||||||||||||||||||||||||	189,4	0.024	193	70,1	77,2	164,3	NA	0|1	0|1	924751_C_A	NA	924751	95,94,1,3	pakistan1_PS-9941-44_tumour
chr1	925895		C	T	NA	PASS	SITE	119,49|4,2	NA	NA	182	1	93	37,20	129,127	60,60	19	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	5.14	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||||||||||	168,6	0.029	174	61,1	62,2	137,4	NA	0/1	NA	NA	NA	NA	119,49,4,2	pakistan1_PS-9941-44_tumour
chr1	930282		G	A	NA	PASS	SITE	163,272|2,7	NA	NA	457	1	93	37,37	123,104	60,60	7	NA	NA	NA	NA	NA	3.05	12	NA	NA	NA	NA	NA	NA	14.11	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||||||||||	435,9	0.023	444	157,4	167,2	342,7	NA	0/1	NA	NA	NA	NA	163,272,2,7	pakistan1_PS-9941-44_tumour
chr1	930911		C	T	NA	PASS	SITE	32,6|4,0	NA	NA	43	2	72	37,37	166,248	60,60	4	NA	NA	NA	NA	NA	4.61	9	NA	NA	NA	NA	NA	NA	10.35	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|||||||	38,4	0.131	42	8,3	24,1	32,4	NA	0/1	NA	NA	NA	NA	32,6,4,0	pakistan1_PS-9941-44_tumour
chr1	935902		G	A	NA	PASS	SITE	56,193|1,5	NA	NA	269	2	93	37,37	133,156	60,60	4	NA	NA	NA	NA	NA	7.3	17	NA	NA	NA	NA	NA	NA	9.5	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||||||||||||||||||||||||||||||||||||||||||||||||	249,6	0.026	255	99,3	104,2	225,5	NA	0/1	NA	NA	NA	NA	56,193,1,5	pakistan1_PS-9941-44_tumour
chr1	939602		TG	T	NA	PASS	SITE	0,1|1,2	NA	NA	4	2	18	37,20	171,185	60,60	36	NA	NA	NA	NA	NA	7.3	93	4,3	G	NA	true	NA	93	5.2	-	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||||||||||||||||||||||||||||||||||||	1,3	0.604	4	0,1	0,0	1,2	NA	0/1	NA	NA	NA	NA	0,1,1,2	pakistan1_PS-9941-44_tumour
chr1	941365		T	C	NA	PASS	SITE	7,42|0,4	NA	NA	53	1	93	37,37	146,215	60,60	19	NA	NA	NA	NA	NA	7.3	32	NA	NA	NA	NA	NA	NA	9.78	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|	49,4	0.102	53	18,2	23,2	43,4	NA	0/1	NA	NA	NA	NA	7,42,0,4	pakistan1_PS-9941-44_tumour
chr1	941507		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,258	60,60	23	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	3.88	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|	0,1	0.667	1	0,0	0,0	0,1	NA	0/1	NA	NA	NA	NA	0,0,0,1	pakistan1_PS-9941-44_tumour
chr1	942032		C	T	NA	PASS	SITE	5,0|2,0	NA	NA	7	2	30	37,37	157,188	60,60	8	NA	NA	NA	NA	NA	7.3	18	NA	NA	NA	NA	NA	NA	6.13	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||||||||||||||||||||||||||||||||||||||||||||||||	5,2	0.333	7	4,1	1,1	5,2	NA	0/1	NA	NA	NA	NA	5,0,2,0	pakistan1_PS-9941-44_tumour
chr1	943587		C	T	NA	PASS	SITE	7,1|3,0	NA	NA	11	2	6	37,37	210,152	60,60	8	NA	NA	NA	NA	NA	4.61	19	NA	NA	NA	NA	NA	NA	9.43	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||||||||||||||||||||||||||||||||||||||||||||||||	8,3	0.338	11	6,1	0,2	7,3	NA	0/1	NA	NA	NA	NA	7,1,3,0	pakistan1_PS-9941-44_tumour
chr1	945622		C	T	NA	PASS	SITE	50,90|5,3	NA	NA	152	1	93	37,20	131,170	54,60	69	NA	NA	NA	NA	NA	7.3	18	NA	NA	NA	NA	NA	NA	12.73	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|||||||	140,8	0.05	148	59,2	52,3	113,5	NA	0/1	NA	NA	NA	NA	50,90,5,3	pakistan1_PS-9941-44_tumour
chr1	946068		C	T	NA	PASS	SITE	8,3|2,0	NA	NA	20	1	45	20,37	154,167	60,60	4	NA	NA	NA	NA	NA	7.3	3	NA	NA	NA	NA	NA	NA	5.66	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||||||||||||||||||||||||||||||||||||	11,2	0.264	13	0,2	7,0	7,2	NA	0/1	NA	NA	NA	NA	8,3,2,0	pakistan1_PS-9941-44_tumour
chr1	956211		C	T	NA	PASS	SITE	47,161|2,2	NA	NA	213	1	93	37,20	136,191	60,60	68	NA	NA	NA	NA	NA	3.12	6	NA	NA	NA	NA	NA	NA	3.46	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|||||||	208,4	0.017	212	76,1	90,1	173,2	NA	0/1	NA	NA	NA	NA	47,161,2,2	pakistan1_PS-9941-44_tumour
chr1	956311		C	G	NA	PASS	SITE	3,12|1,3	NA	NA	21	1	41	37,29	191,241	60,60	25	NA	NA	NA	NA	NA	7.3	34	NA	NA	NA	NA	NA	NA	9.7	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||||||||||||||||||||||||||||||||||||||||||	15,4	0.235	19	6,2	5,1	12,3	NA	0/1	NA	NA	NA	NA	3,12,1,3	pakistan1_PS-9941-44_tumour
chr1	956663		A	G	NA	PASS	SITE	12,1|3,0	NA	NA	16	1	42	37,37	207,180	60,60	24	NA	NA	NA	NA	NA	7.3	27	NA	NA	NA	NA	NA	NA	8.67	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||||||||||||||||||||||||||||||||||||||||||	13,3	0.235	16	3,1	9,2	12,3	NA	0/1	NA	NA	NA	NA	12,1,3,0	pakistan1_PS-9941-44_tumour
chr1	963011		C	T	NA	PASS	SITE	3,12|2,0	NA	NA	21	2	28	37,37	210,173	60,60	5	NA	NA	NA	NA	NA	4.61	2	NA	NA	NA	NA	NA	NA	5.09	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||||||||||	15,2	0.174	17	7,0	6,2	13,2	NA	0|1	0|1	963011_C_T	NA	963011	3,12,2,0	pakistan1_PS-9941-44_tumour
chr1	963446		G	A	NA	PASS	SITE	103,123|5,6	NA	NA	241	2	93	37,20	117,161	60,60	6	NA	NA	NA	NA	NA	7.3	9	NA	NA	NA	NA	NA	NA	19.6	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|||||||	226,11	0.044	237	100,2	72,6	191,8	NA	0/1	NA	NA	NA	NA	103,123,5,6	pakistan1_PS-9941-44_tumour
chr1	964969		G	A	NA	PASS	SITE	201,85|2,3	NA	NA	327	2	93	37,20	126,88	60,60	12	NA	NA	NA	NA	NA	4.13	4	NA	NA	NA	NA	NA	NA	5.27	A	synonymous_variant	LOW	KLHL17	ENSG00000187961	Transcript	ENST00000338591	protein_coding	12/12		ENST00000338591.8:c.1707G>A	ENSP00000343930.3:p.Thr569=	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||||||||||	286,5	0.016	291	120,2	114,1	239,3	NA	0/1	NA	NA	NA	NA	201,85,2,3	pakistan1_PS-9941-44_tumour
chr1	966767		C	G	NA	PASS	SITE	91,169|3,5	NA	NA	285	1	93	37,20	115,163	60,60	11	NA	NA	NA	NA	NA	7.3	51	NA	NA	NA	NA	NA	NA	10.89	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=|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=|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=|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|	260,8	0.026	268	121,2	100,3	227,5	NA	0/1	NA	NA	NA	NA	91,169,3,5	pakistan1_PS-9941-44_tumour
chr1	972943		G	A	NA	PASS	SITE	141,108|3,1	NA	NA	266	1	93	37,29	123,79	60,60	19	NA	NA	NA	NA	NA	2.06	4	NA	NA	NA	NA	NA	NA	4.78	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|||||||	249,4	0.019	253	111,2	92,1	208,3	NA	0/1	NA	NA	NA	NA	141,108,3,1	pakistan1_PS-9941-44_tumour
chr1	974495		G	A	NA	PASS	SITE	98,66|3,5	NA	NA	180	1	93	37,37	130,124	60,60	2	NA	NA	NA	NA	NA	2.85	15	NA	NA	NA	NA	NA	NA	16.47	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||||||||||	164,8	0.047	172	66,4	74,2	144,7	NA	0/1	NA	NA	NA	NA	98,66,3,5	pakistan1_PS-9941-44_tumour
chr1	980177		A	C	NA	PASS	SITE	84,148|5,2	NA	NA	255	1	93	37,20	138,212	60,60	27	NA	NA	NA	NA	NA	7.3	4	NA	NA	NA	NA	NA	NA	9.34	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||||||||||||||||||||||||||||||||||||	232,7	0.029	239	82,0	103,5	200,5	NA	0/1	NA	NA	NA	NA	84,148,5,2	pakistan1_PS-9941-44_tumour
chr1	981651		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,172	60,60	19	NA	NA	NA	NA	NA	7.3	9	NA	NA	NA	NA	NA	NA	3.88	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||||||||||||||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	981866		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,212	60,60	4	NA	NA	NA	NA	NA	7.3	7	NA	NA	NA	NA	NA	NA	3.87	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||||||||||||||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,1	0,0	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1013876		G	T	NA	PASS	SITE	24,5|2,0	NA	NA	36	2	93	25,37	186,184	60,60	15	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	4.4	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||||||||||||||||||||||||||||||||||||||||||||||||	29,2	0.107	31	13,2	9,0	24,2	NA	0/1	NA	NA	NA	NA	24,5,2,0	pakistan1_PS-9941-44_tumour
chr1	1014052		G	A	NA	PASS	SITE	275,286|4,5	NA	NA	610	2	93	37,37	125,130	60,60	27	NA	NA	NA	NA	NA	4.31	6	NA	NA	NA	NA	NA	NA	16.33	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=|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=|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=|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||||||||||	561,9	0.021	570	223,7	239,2	471,9	NA	0/1	NA	NA	NA	NA	275,286,4,5	pakistan1_PS-9941-44_tumour
chr1	1014451		C	T	NA	PASS	SITE	155,273|5,5	NA	NA	444	1	93	37,20	126,69	60,60	17	NA	NA	NA	NA	NA	1.96	8	NA	NA	NA	NA	NA	NA	14.74	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=|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=|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|||||||	428,10	0.022	438	168,5	169,2	353,7	NA	0/1	NA	NA	NA	NA	155,273,5,5	pakistan1_PS-9941-44_tumour
chr1	1017131		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,0	60,41	3	NA	NA	NA	NA	NA	7.3	11	NA	NA	NA	NA	NA	NA	3.88	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||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,0,1	pakistan1_PS-9941-44_tumour
chr1	1033312		C	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	2	31	0,37	0,103	60,60	24	NA	NA	NA	NA	NA	7.3	16	NA	NA	NA	NA	NA	NA	3.88	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|	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1033323		C	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	2	31	0,37	0,103	60,60	19	NA	NA	NA	NA	NA	7.3	16	NA	NA	NA	NA	NA	NA	3.88	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|	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1044428		G	A	NA	PASS	SITE	84,138|2,6	NA	NA	253	1	93	37,20	120,134	60,60	5	NA	NA	NA	NA	NA	7.3	18	NA	NA	NA	NA	NA	NA	10.76	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||||||||||	222,8	0.033	230	100,3	73,2	181,6	NA	0/1	NA	NA	NA	NA	84,138,2,6	pakistan1_PS-9941-44_tumour
chr1	1045491		G	A	NA	PASS	SITE	83,124|7,7	NA	NA	224	1	93	37,20	121,87	60,60	10	NA	NA	NA	NA	NA	7.3	17	NA	NA	NA	NA	NA	NA	19.45	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|||||||||||||||||||||||||||||||	207,14	0.047	221	53,5	38,2	161,7	NA	0/1	NA	NA	NA	NA	83,124,7,7	pakistan1_PS-9941-44_tumour
chr1	1047806		G	A	NA	PASS	SITE	131,134|2,4	NA	NA	282	1	93	37,20	130,134	60,60	30	NA	NA	NA	NA	NA	4.31	2	NA	NA	NA	NA	NA	NA	7.7	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|||||||	265,6	0.021	271	109,1	108,3	229,4	NA	0/1	NA	NA	NA	NA	131,134,2,4	pakistan1_PS-9941-44_tumour
chr1	1048100		G	A	NA	PASS	SITE	102,226|2,6	NA	NA	367	2	93	37,29	120,94	60,60	27	NA	NA	NA	NA	NA	4.61	7	NA	NA	NA	NA	NA	NA	12.2	A	synonymous_variant	LOW	AGRN	ENSG00000188157	Transcript	ENST00000379370	protein_coding	23/36		ENST00000379370.7:c.3840G>A	ENSP00000368678.2:p.Pro1280=	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=|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=|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=|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|||||||	328,8	0.024	336	79,1	53,1	285,6	NA	0/1	NA	NA	NA	NA	102,226,2,6	pakistan1_PS-9941-44_tumour
chr1	1050276		C	T	NA	PASS	SITE	158,149|3,4	NA	NA	333	1	93	37,37	121,103	60,60	23	NA	NA	NA	NA	NA	4.31	12	NA	NA	NA	NA	NA	NA	11.54	T	synonymous_variant	LOW	AGRN	ENSG00000188157	Transcript	ENST00000379370	protein_coding	28/36		ENST00000379370.7:c.4923C>T	ENSP00000368678.2:p.Asn1641=	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=|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=|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=|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||||||||||	307,7	0.028	314	113,4	120,2	239,6	NA	0/1	NA	NA	NA	NA	158,149,3,4	pakistan1_PS-9941-44_tumour
chr1	1054333		G	A	NA	PASS	SITE	11,4|3,0	NA	NA	19	1	47	20,37	162,232	60,60	15	NA	NA	NA	NA	NA	7.3	17	NA	NA	NA	NA	NA	NA	8.79	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|||||||	15,3	0.251	18	5,2	5,1	11,3	NA	0/1	NA	NA	NA	NA	11,4,3,0	pakistan1_PS-9941-44_tumour
chr1	1087520		C	T	NA	PASS	SITE	274,114|3,3	NA	NA	420	2	93	37,37	124,91	60,60	9	NA	NA	NA	NA	NA	4.13	4	NA	NA	NA	NA	NA	NA	8.49	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||||||||||	388,6	0.018	394	145,1	145,2	330,5	NA	0/1	NA	NA	NA	NA	274,114,3,3	pakistan1_PS-9941-44_tumour
chr1	1090856		C	T	NA	PASS	SITE	131,42|6,2	NA	NA	182	1	93	37,29	122,167	60,60	8	NA	NA	NA	NA	NA	4.61	2	NA	NA	NA	NA	NA	NA	14.25	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||||||||||	173,8	0.046	181	81,1	63,5	144,6	NA	0/1	NA	NA	NA	NA	131,42,6,2	pakistan1_PS-9941-44_tumour
chr1	1127102		AC	GT	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,97	60,39	9	NA	NA	NA	NA	NA	7.3	7	NA	NA	NA	NA	NA	NA	4.2	GT	intergenic_variant	MODIFIER																			substitution																																																	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,0,1	pakistan1_PS-9941-44_tumour
chr1	1137055		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	2	31	0,37	0,134	60,60	23	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	3.88	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||||||||||||||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1138185		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	2	1	32	0,37	0,133	60,60	11	NA	NA	NA	NA	NA	7.3	7	NA	NA	NA	NA	NA	NA	7.88	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																																											0,2	0.75	2	0,0	0,2	0,2	NA	0/1	NA	NA	NA	NA	0,0,2,0	pakistan1_PS-9941-44_tumour
chr1	1179527		C	T	NA	PASS	SITE	13,1|2,0	NA	NA	18	2	52	37,37	207,159	60,60	15	NA	NA	NA	NA	NA	7.3	15	NA	NA	NA	NA	NA	NA	5.1	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|||||||	14,2	0.174	16	9,1	4,1	13,2	NA	0|1	0|1	1179527_C_T	NA	1179527	13,1,2,0	pakistan1_PS-9941-44_tumour
chr1	1179532		C	T	NA	PASS	SITE	8,1|6,0	NA	NA	15	2	24	37,37	192,207	60,60	7	NA	NA	NA	NA	NA	7.3	28	NA	NA	NA	NA	NA	NA	19.21	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|||||||	9,6	0.437	15	5,4	3,2	8,6	NA	1|0	1|0	1179527_C_T	NA	1179527	8,1,6,0	pakistan1_PS-9941-44_tumour
chr1	1180783		C	T	NA	PASS	SITE	78,65|2,2	NA	NA	154	1	93	37,29	116,122	60,60	27	NA	NA	NA	NA	NA	7.3	5	NA	NA	NA	NA	NA	NA	5.73	T	synonymous_variant	LOW	TTLL10	ENSG00000162571	Transcript	ENST00000379288	protein_coding	4/9		ENST00000379288.3:c.459C>T	ENSP00000368590.3:p.Ile153=	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=|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=|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|||||||	143,4	0.033	147	41,2	64,1	114,3	NA	0/1	NA	NA	NA	NA	78,65,2,2	pakistan1_PS-9941-44_tumour
chr1	1182517		CT	C	NA	PASS	SITE	10,68|1,3	NA	NA	84	1	93	37,29	159,135	60,60	27	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	5.55	-	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||||||||||||||||||||||||||||||||||||	78,4	0.054	82	20,1	22,0	68,3	NA	0/1	NA	NA	NA	NA	10,68,1,3	pakistan1_PS-9941-44_tumour
chr1	1185203		G	A	NA	PASS	SITE	5,57|0,3	NA	NA	65	1	93	37,37	136,144	60,60	25	NA	NA	NA	NA	NA	4.31	8	NA	NA	NA	NA	NA	NA	6.21	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|	62,3	0.064	65	22,1	35,2	57,3	NA	0/1	NA	NA	NA	NA	5,57,0,3	pakistan1_PS-9941-44_tumour
chr1	1196891		A	AGGGGG	NA	PASS	SITE	1,5|0,2	NA	NA	9	1	12	37,29	261,210	60,60	7	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	6.58	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||||||||||||||||||||||||||||||||||||||||||||||||	6,2	0.3	8	1,1	5,1	6,2	NA	0/1	NA	NA	NA	NA	1,5,0,2	pakistan1_PS-9941-44_tumour
chr1	1204533		G	A	NA	PASS	SITE	10,34|0,3	NA	NA	47	2	93	37,37	130,134	60,60	17	NA	NA	NA	NA	NA	7.3	3	NA	NA	NA	NA	NA	NA	5.65	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||||||||||||||||||||||||||||||||||||||||||||||||	44,3	0.08	47	7,0	4,0	44,3	NA	0/1	NA	NA	NA	NA	10,34,0,3	pakistan1_PS-9941-44_tumour
chr1	1205436		C	T	NA	PASS	SITE	169,130|2,1	NA	NA	320	2	93	37,20	129,132	60,60	43	NA	NA	NA	NA	NA	7.3	5	NA	NA	NA	NA	NA	NA	6.51	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|||||||	299,3	0.011	302	111,1	109,1	266,2	NA	0|1	0|1	1205419_C_T	NA	1205419	169,130,2,1	pakistan1_PS-9941-44_tumour
chr1	1212158		G	A	NA	PASS	SITE	15,83|1,5	NA	NA	105	2	93	37,37	139,152	60,60	23	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	13.09	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||||||||||	98,6	0.076	104	36,1	44,5	84,6	NA	0|1	0|1	1212158_G_A	NA	1212158	15,83,1,5	pakistan1_PS-9941-44_tumour
chr1	1212180		T	C	NA	PASS	SITE	3,60|0,2	NA	NA	66	2	93	37,37	141,146	60,60	24	NA	NA	NA	NA	NA	7.3	2	NA	NA	NA	NA	NA	NA	3.25	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||||||||||	63,2	0.046	65	16,0	39,2	60,2	NA	1|0	1|0	1212158_G_A	NA	1212158	3,60,0,2	pakistan1_PS-9941-44_tumour
chr1	1212957		C	T	NA	PASS	SITE	145,26|2,2	NA	NA	190	2	93	37,20	139,260	60,60	79	NA	NA	NA	NA	NA	7.3	9	NA	NA	NA	NA	NA	NA	3.59	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||||||||||||||||||||||||||||||||||||||||||||||||	171,4	0.019	175	79,1	69,1	152,2	NA	0/1	NA	NA	NA	NA	145,26,2,2	pakistan1_PS-9941-44_tumour
chr1	1217308		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	1	2	31	0,37	0,192	60,60	20	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	3.88	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||||||||||||||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,1	0,0	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1217431		C	T	NA	PASS	SITE	38,7|3,1	NA	NA	58	1	93	37,29	152,123	60,60	7	NA	NA	NA	NA	NA	7.3	11	NA	NA	NA	NA	NA	NA	7.54	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||||||||||||||||||||||||||||||||||||||||||||||||	45,4	0.089	49	21,1	18,2	39,3	NA	0/1	NA	NA	NA	NA	38,7,3,1	pakistan1_PS-9941-44_tumour
chr1	1223443		C	A	NA	PASS	SITE	1,2|0,2	NA	NA	5	1	27	37,37	159,225	60,60	3	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	6.58	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|||||||||||||||||||||||||||||||||||	3,2	0.429	5	2,2	1,0	3,2	NA	0/1	NA	NA	NA	NA	1,2,0,2	pakistan1_PS-9941-44_tumour
chr1	1223969		C	CCCATTTGCTGTCTTGCAGGG	NA	PASS	SITE	21,83|0,4	NA	NA	118	2	93	37,37	129,83	60,60	22	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	9.08	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|||||||||||||||||||||||||||||||||||	104,4	0.047	108	21,0	29,1	128,4	NA	0|1	0|1	1223968_C_CTG	NA	1223968	21,83,0,4	pakistan1_PS-9941-44_tumour
chr1	1228504		C	T	NA	PASS	SITE	177,112|8,2	NA	NA	322	2	93	37,37	137,163	60,60	26	NA	NA	NA	NA	NA	4.31	9	NA	NA	NA	NA	NA	NA	18.45	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||||||||||	289,10	0.039	299	70,6	112,2	242,9	NA	0/1	NA	NA	NA	NA	177,112,8,2	pakistan1_PS-9941-44_tumour
chr1	1231926		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	2	1	32	0,20	0,102	60,60	15	NA	NA	NA	NA	NA	7.3	5	NA	NA	NA	NA	NA	NA	4.62	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|	0,2	0.667	2	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,1	pakistan1_PS-9941-44_tumour
chr1	1233361		C	CG	NA	PASS	SITE	4,14|0,3	NA	NA	23	2	36	37,37	198,129	60,60	5	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	9.38	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||||||||||||||||||||||||||||||||||||||||||||||||	18,3	0.208	21	5,2	6,1	14,3	NA	0|1	0|1	1233361_C_CG	NA	1233361	4,14,0,3	pakistan1_PS-9941-44_tumour
chr1	1233364		C	G	NA	PASS	SITE	4,14|0,3	NA	NA	21	2	55	37,37	198,129	60,60	1	NA	NA	NA	NA	NA	7.3	40	NA	NA	NA	NA	NA	NA	9.4	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||||||||||||||||||||||||||||||||||||||||||||||||	18,3	0.21	21	4,2	2,1	14,3	NA	0|1	0|1	1233361_C_CG	NA	1233361	4,14,0,3	pakistan1_PS-9941-44_tumour
chr1	1242769		C	T	NA	PASS	SITE	50,16|21,10	NA	NA	109	1	10	37,37	147,151	60,60	14	NA	NA	NA	NA	NA	3.53	84	NA	NA	NA	NA	NA	NA	88.54	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||||||||||	66,31	0.328	97	32,11	23,15	56,27	NA	0/1	NA	NA	NA	NA	50,16,21,10	pakistan1_PS-9941-44_tumour
chr1	1243520		G	GGTGCCTTCCTGC	NA	PASS	SITE	91,176|2,2	NA	NA	309	2	93	37,37	117,116	60,60	26	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	7.75	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||||||||||||||||||||||||||||||||||||||||||	267,4	0.021	271	68,1	44,1	255,4	NA	0|1	0|1	1243520_G_GGTGCCTTCCTGC	NA	1243520	91,176,2,2	pakistan1_PS-9941-44_tumour
chr1	1243522		A	AGGCTCCGGTCTGAGCCTG	NA	PASS	SITE	91,182|2,2	NA	NA	297	2	93	37,37	117,116	60,60	8	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	7.59	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||||||||||||||||||||||||||||||||||||||||||	273,4	0.02	277	68,1	46,3	257,4	NA	0|1	0|1	1243520_G_GGTGCCTTCCTGC	NA	1243520	91,182,2,2	pakistan1_PS-9941-44_tumour
chr1	1243665		G	A	NA	PASS	SITE	0,6|0,4	NA	NA	10	2	25	37,37	203,216	60,60	18	NA	NA	NA	NA	NA	7.3	34	NA	NA	NA	NA	NA	NA	12.14	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||||||||||||||||||||||||||||||||||||||||||	6,4	0.417	10	3,2	3,2	6,4	NA	0/1	NA	NA	NA	NA	0,6,0,4	pakistan1_PS-9941-44_tumour
chr1	1243997		C	T	NA	PASS	SITE	145,94|4,2	NA	NA	256	2	93	37,20	127,155	60,60	10	NA	NA	NA	NA	NA	4.01	16	NA	NA	NA	NA	NA	NA	7.91	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||||||||||	239,6	0.023	245	81,2	110,2	207,4	NA	0/1	NA	NA	NA	NA	145,94,4,2	pakistan1_PS-9941-44_tumour
chr1	1246138		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,115	60,60	18	NA	NA	NA	NA	NA	7.3	10	NA	NA	NA	NA	NA	NA	3.88	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|||||||||||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1257001		C	T	NA	PASS	SITE	107,41|4,1	NA	NA	166	1	93	37,37	128,142	60,60	20	NA	NA	NA	NA	NA	7.3	18	NA	NA	NA	NA	NA	NA	8.26	T	synonymous_variant	LOW	UBE2J2	ENSG00000160087	Transcript	ENST00000347370	protein_coding	5/7		ENST00000347370.6:c.249G>A	ENSP00000344857.2:p.Ser83=	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=|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=|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=|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=|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=|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=|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|||||||	148,5	0.038	153	61,2	60,2	126,4	NA	0/1	NA	NA	NA	NA	107,41,4,1	pakistan1_PS-9941-44_tumour
chr1	1267175		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,85	60,56	27	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	3.88	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||||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1267740		G	T	NA	PASS	SITE	8,3|2,0	NA	NA	15	1	45	37,37	231,176	60,60	10	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	5.5	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||||||||||||||||||||||||||||||||||||||||||||||||	11,2	0.228	13	2,2	7,0	9,2	NA	0/1	NA	NA	NA	NA	8,3,2,0	pakistan1_PS-9941-44_tumour
chr1	1285877		G	T	NA	PASS	SITE	38,12|6,0	NA	NA	78	1	93	37,37	130,171	60,60	5	NA	NA	NA	NA	NA	7.3	2	NA	NA	NA	NA	NA	NA	16.41	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||||||||||||||||||||||||||||||||||||	50,6	0.147	56	16,0	23,6	39,6	NA	0/1	NA	NA	NA	NA	38,12,6,0	pakistan1_PS-9941-44_tumour
chr1	1286305		G	A	NA	PASS	SITE	11,81|4,7	NA	NA	117	1	93	37,37	143,214	60,60	3	NA	NA	NA	NA	NA	7.3	18	NA	NA	NA	NA	NA	NA	33.91	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||||||||||||||||||||||||||||||||||||	92,11	0.085	103	39,5	43,2	84,7	NA	0/1	NA	NA	NA	NA	11,81,4,7	pakistan1_PS-9941-44_tumour
chr1	1286678		G	C	NA	PASS	SITE	34,6|2,0	NA	NA	42	1	93	37,37	165,122	60,60	5	NA	NA	NA	NA	NA	7.3	4	NA	NA	NA	NA	NA	NA	3.99	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||||||||||||||||||||||||||||||||||||	40,2	0.079	42	18,0	15,2	34,2	NA	0/1	NA	NA	NA	NA	34,6,2,0	pakistan1_PS-9941-44_tumour
chr1	1287462		C	T	NA	PASS	SITE	102,17|6,3	NA	NA	134	2	93	37,20	159,168	60,60	32	NA	NA	NA	NA	NA	2.58	16	NA	NA	NA	NA	NA	NA	15.98	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||||||||||	119,9	0.062	128	49,2	54,4	104,6	NA	0|1	0|1	1287462_C_T	NA	1287462	102,17,6,3	pakistan1_PS-9941-44_tumour
chr1	1287464		C	T	NA	PASS	SITE	105,19|3,1	NA	NA	133	2	93	37,29	159,176	60,60	27	NA	NA	NA	NA	NA	3.46	5	NA	NA	NA	NA	NA	NA	5.91	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||||||||||	124,4	0.036	128	49,2	56,1	107,3	NA	1|0	1|0	1287462_C_T	NA	1287462	105,19,3,1	pakistan1_PS-9941-44_tumour
chr1	1290571		TG	T	NA	PASS	SITE	147,147|6,3	NA	NA	351	2	93	37,20	136,104	60,60	26	NA	NA	NA	NA	NA	7.3	93	4,3	G	NA	true	NA	93	3.82	-	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||||||||||||||||||||||||||||||||||||||||||||||||	294,9	0.024	303	87,0	81,6	242,6	NA	0|1	0|1	1290571_TG_T	NA	1290571	147,147,6,3	pakistan1_PS-9941-44_tumour
chr1	1291449		C	T	NA	PASS	SITE	129,117|7,3	NA	NA	277	2	93	37,37	120,168	60,60	8	NA	NA	NA	NA	NA	7.3	13	NA	NA	NA	NA	NA	NA	20.51	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||||||||||||||||||||||||||||||||||||||||||||||||	246,10	0.045	256	63,5	90,2	212,9	NA	0/1	NA	NA	NA	NA	129,117,7,3	pakistan1_PS-9941-44_tumour
chr1	1293731		A	ACGCCCCTGCCCTGGAGGCCC	NA	PASS	SITE	0,0|1,7	NA	NA	91	1	15	0,20	0,216	60,60	96	NA	NA	NA	NA	NA	7.3	93	3,4	CGCCCCTGCCCTGGAGGCCC	NA	true	NA	11	26.77	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||||||||||	0,8	0.671	8	0,3	0,2	0,9	NA	0/1	NA	NA	NA	NA	0,0,1,7	pakistan1_PS-9941-44_tumour
chr1	1296753		G	A	NA	PASS	SITE	0,2|2,6	NA	NA	10	1	29	37,29	304,226	60,60	5	NA	NA	NA	NA	NA	7.3	35	NA	NA	NA	NA	NA	NA	22.43	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|||||||||||||||||||||||||||||||||||||||||||||	2,8	0.7	10	2,2	0,3	2,6	NA	0/1	NA	NA	NA	NA	0,2,2,6	pakistan1_PS-9941-44_tumour
chr1	1298150		AC	A	NA	PASS	SITE	19,136|2,6	NA	NA	176	1	93	37,20	138,114	60,60	23	NA	NA	NA	NA	NA	7.3	93	2,1	C	NA	true	NA	93	9.7	-	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||||||||||||||||||||||||||||||||||||||||||||||||	155,8	0.048	163	33,3	20,0	137,6	NA	0/1	NA	NA	NA	NA	19,136,2,6	pakistan1_PS-9941-44_tumour
chr1	1298712		AC	A	NA	PASS	SITE	18,101|1,4	NA	NA	152	1	93	37,37	134,175	60,60	14	NA	NA	NA	NA	NA	7.3	93	4,3	C	NA	true	NA	93	4.43	-	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|||||||||||||||||||||||||||||||||||||||||||||	119,5	0.045	124	22,4	25,0	101,4	NA	0/1	NA	NA	NA	NA	18,101,1,4	pakistan1_PS-9941-44_tumour
chr1	1300764		G	A	NA	PASS	SITE	6,42|0,2	NA	NA	50	2	93	37,37	144,148	60,60	9	NA	NA	NA	NA	NA	4.31	11	NA	NA	NA	NA	NA	NA	3.73	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||||||||||||||||||||||||||||||||||||||||||||||||	48,2	0.065	50	16,1	26,1	42,2	NA	0/1	NA	NA	NA	NA	6,42,0,2	pakistan1_PS-9941-44_tumour
chr1	1304054		C	T	NA	PASS	SITE	197,34|3,1	NA	NA	252	1	93	37,29	125,120	60,60	27	NA	NA	NA	NA	NA	4.01	3	NA	NA	NA	NA	NA	NA	4.79	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||||||||||	231,4	0.019	235	92,2	104,1	202,3	NA	0/1	NA	NA	NA	NA	197,34,3,1	pakistan1_PS-9941-44_tumour
chr1	1311463		C	A	NA	PASS	SITE	7,54|2,3	NA	NA	66	1	93	37,20	137,223	60,60	24	NA	NA	NA	NA	NA	7.3	2	NA	NA	NA	NA	NA	NA	4.99	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||||||||||||||||||||||||||||||||||||	61,5	0.056	66	27,2	27,0	54,3	NA	0/1	NA	NA	NA	NA	7,54,2,3	pakistan1_PS-9941-44_tumour
chr1	1312290		C	T	NA	PASS	SITE	130,100|3,1	NA	NA	251	2	93	37,23	122,171	60,60	33	NA	NA	NA	NA	NA	4.61	5	NA	NA	NA	NA	NA	NA	3.69	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||||||||||	230,4	0.02	234	57,2	81,1	194,3	NA	0/1	NA	NA	NA	NA	130,100,3,1	pakistan1_PS-9941-44_tumour
chr1	1314368		G	A	NA	PASS	SITE	175,333|4,4	NA	NA	543	1	93	37,20	119,79	60,60	9	NA	NA	NA	NA	NA	7.3	15	NA	NA	NA	NA	NA	NA	6.41	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||||||||||||||||||||||||||||||||||||||||||||||||	508,8	0.012	516	186,2	208,2	415,4	NA	0/1	NA	NA	NA	NA	175,333,4,4	pakistan1_PS-9941-44_tumour
chr1	1324790		GT	AG	NA	PASS	SITE	0,0|0,6	NA	NA	6	1	43	0,37	0,255	60,60	3	NA	NA	NA	NA	NA	7.3	54	NA	NA	NA	NA	NA	NA	21.97	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||||||||||||||||||||||||||||||||||||||||||||||||	0,6	0.869	6	0,4	0,2	0,6	NA	0/1	NA	NA	NA	NA	0,0,0,6	pakistan1_PS-9941-44_tumour
chr1	1331483		C	T	NA	PASS	SITE	80,109|1,5	NA	NA	214	2	93	37,37	126,134	60,60	2	NA	NA	NA	NA	NA	3.83	2	NA	NA	NA	NA	NA	NA	10.31	T	synonymous_variant	LOW	TAS1R3	ENSG00000169962	Transcript	ENST00000339381	protein_coding	1/6		ENST00000339381.6:c.138C>T	ENSP00000344411.5:p.Ala46=	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|||||||	189,6	0.035	195	76,4	81,1	165,5	NA	0/1	NA	NA	NA	NA	80,109,1,5	pakistan1_PS-9941-44_tumour
chr1	1333592		GC	G	NA	PASS	SITE	179,217|2,5	NA	NA	426	2	93	37,20	129,163	60,60	52	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	4.53	-	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||||||||||||||||||||||||||||||||||||||||||||||||	396,7	0.015	403	91,2	94,0	326,5	NA	0/1	NA	NA	NA	NA	179,217,2,5	pakistan1_PS-9941-44_tumour
chr1	1336588		G	A	NA	PASS	SITE	2,26|0,2	NA	NA	31	1	63	37,37	159,150	60,60	20	NA	NA	NA	NA	NA	4.61	12	NA	NA	NA	NA	NA	NA	4.31	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||||||||||||||||||||||||||||||||||	28,2	0.1	30	12,1	14,1	26,2	NA	0/1	NA	NA	NA	NA	2,26,0,2	pakistan1_PS-9941-44_tumour
chr1	1337030		C	T	NA	PASS	SITE	178,96|2,3	NA	NA	285	2	93	37,37	138,134	60,60	16	NA	NA	NA	NA	NA	7.3	5	NA	NA	NA	NA	NA	NA	6.91	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||||||||||||||||||||||||||||||||||	274,5	0.02	279	101,1	85,1	240,4	NA	1|0	1|0	1337018_C_T	NA	1337018	178,96,2,3	pakistan1_PS-9941-44_tumour
chr1	1339367		C	T	NA	PASS	SITE	230,321|3,6	NA	NA	579	2	93	37,37	119,152	60,60	2	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	12.33	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||||||||||	551,9	0.017	560	207,2	237,5	469,8	NA	0|1	0|1	1339367_C_T	NA	1339367	230,321,3,6	pakistan1_PS-9941-44_tumour
chr1	1339610		C	T	NA	PASS	SITE	83,49|3,1	NA	NA	150	1	93	37,29	124,122	60,60	26	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	5.83	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=|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=|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=|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||||||||||	132,4	0.034	136	39,1	62,2	111,3	NA	0/1	NA	NA	NA	NA	83,49,3,1	pakistan1_PS-9941-44_tumour
chr1	1340417		G	A	NA	PASS	SITE	206,185|4,4	NA	NA	417	1	93	37,20	126,136	60,60	63	NA	NA	NA	NA	NA	7.3	2	NA	NA	NA	NA	NA	NA	8.51	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||||||||||	391,8	0.015	399	156,3	168,1	334,4	NA	0/1	NA	NA	NA	NA	206,185,4,4	pakistan1_PS-9941-44_tumour
chr1	1354171		G	GTGCCCCCCTCCC	NA	PASS	SITE	42,78|0,3	NA	NA	123	2	93	37,37	143,115	60,60	22	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	5.98	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||||||||||||||||||||||||||||||||||||||||||||||||	120,3	0.035	123	26,0	35,0	111,3	NA	0|1	0|1	1354171_G_GTGCCCCCCTCCC	NA	1354171	42,78,0,3	pakistan1_PS-9941-44_tumour
chr1	1354175		C	CCTCCT	NA	PASS	SITE	44,80|0,3	NA	NA	132	2	93	37,37	143,115	60,60	6	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	5.92	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||||||||||||||||||||||||||||||||||||||||||||||||	124,3	0.035	127	27,0	33,0	115,3	NA	0|1	0|1	1354171_G_GTGCCCCCCTCCC	NA	1354171	44,80,0,3	pakistan1_PS-9941-44_tumour
chr1	1355492		C	T	NA	PASS	SITE	111,56|3,1	NA	NA	179	1	93	37,29	121,136	60,60	11	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	5.36	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||||||||||||||||||||||||||||||||||||||||||||||||	167,4	0.026	171	76,2	65,1	146,3	NA	0/1	NA	NA	NA	NA	111,56,3,1	pakistan1_PS-9941-44_tumour
chr1	1356892		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	3	1	32	0,37	0,178	60,60	2	NA	NA	NA	NA	NA	7.3	10	NA	NA	NA	NA	NA	NA	7.45	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||||||||||||||||||||||||||||||||||||||||||||||||	0,2	0.764	2	0,2	0,0	0,2	NA	0/1	NA	NA	NA	NA	0,0,0,2	pakistan1_PS-9941-44_tumour
chr1	1364790		T	C	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,96	60,40	4	NA	NA	NA	NA	NA	7.3	20	NA	NA	NA	NA	NA	NA	3.88	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																																				0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1373781		C	T	NA	PASS	SITE	138,26|3,2	NA	NA	191	1	93	37,20	123,135	60,60	36	NA	NA	NA	NA	NA	4.61	4	NA	NA	NA	NA	NA	NA	6.1	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||||||||||	164,5	0.026	169	55,2	88,1	147,3	NA	0/1	NA	NA	NA	NA	138,26,3,2	pakistan1_PS-9941-44_tumour
chr1	1392922		A	G	NA	PASS	SITE	6,25|1,3	NA	NA	35	1	80	37,23	165,136	60,60	26	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	7.02	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||||||||||||||||||||||||||||||||||||||||||	31,4	0.133	35	17,3	8,0	25,3	NA	0/1	NA	NA	NA	NA	6,25,1,3	pakistan1_PS-9941-44_tumour
chr1	1407259		C	A	NA	PASS	SITE	29,176|2,8	NA	NA	221	2	93	37,29	146,168	60,60	15	NA	NA	NA	NA	NA	7.3	50	NA	NA	NA	NA	NA	NA	16.51	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|	205,10	0.044	215	87,4	61,3	178,8	NA	0/1	NA	NA	NA	NA	29,176,2,8	pakistan1_PS-9941-44_tumour
chr1	1423537		G	A	NA	PASS	SITE	0,0|0,0	NA	NA	2	1	32	0,20	0,60	60,54	24	NA	NA	NA	NA	NA	7.3	9	NA	NA	NA	NA	NA	NA	4.62	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|||||||||||||||||||||||||||||||||||	0,2	0.667	2	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,1	pakistan1_PS-9941-44_tumour
chr1	1437558		G	A	NA	PASS	SITE	3,20|1,3	NA	NA	34	2	60	37,29	167,167	60,60	17	NA	NA	NA	NA	NA	7.3	15	NA	NA	NA	NA	NA	NA	8.5	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||||||||||||||||||||||||||||||||||||||||||||||||	23,4	0.151	27	12,2	9,1	21,3	NA	0/1	NA	NA	NA	NA	3,20,1,3	pakistan1_PS-9941-44_tumour
chr1	1452460		G	GCCCCTCA	NA	PASS	SITE	36,113|0,4	NA	NA	163	2	93	37,37	135,217	40,40	18	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	8.56	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||||||||||||||||||||||||||||||||||||	149,4	0.034	153	35,1	43,3	133,4	NA	0|1	0|1	1452460_G_GCCCCTCA	NA	1452460	36,113,0,4	pakistan1_PS-9941-44_tumour
chr1	1452461		G	GCCACCTGC	NA	PASS	SITE	36,113|0,4	NA	NA	161	2	93	37,37	135,217	40,40	10	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	8.57	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||||||||||||||||||||||||||||||||||||	149,4	0.034	153	35,1	43,3	133,4	NA	0|1	0|1	1452460_G_GCCCCTCA	NA	1452460	36,113,0,4	pakistan1_PS-9941-44_tumour
chr1	1455403		GGTGGCTGTTCC	G	NA	PASS	SITE	72,19|6,1	NA	NA	123	2	93	37,37	119,159	54,60	19	NA	NA	NA	NA	NA	7.3	93	NA	NA	NA	NA	NA	NA	21.15	-	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||||||||||||||||||||||||||||||||||||	91,7	0.084	98	28,0	27,6	79,6	NA	0/1	NA	NA	NA	NA	72,19,6,1	pakistan1_PS-9941-44_tumour
chr1	1455662		G	A	NA	PASS	SITE	9,9|2,3	NA	NA	24	1	42	37,20	195,264	60,60	19	NA	NA	NA	NA	NA	7.3	3	NA	NA	NA	NA	NA	NA	10.01	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||||||||||||||||||||||||||||||||||||	18,5	0.19	23	7,0	9,3	16,3	NA	0/1	NA	NA	NA	NA	9,9,2,3	pakistan1_PS-9941-44_tumour
chr1	1457166		C	A	NA	PASS	SITE	55,101|1,5	NA	NA	181	2	93	37,37	126,167	52,45	9	NA	NA	NA	NA	NA	7.3	6	NA	NA	NA	NA	NA	NA	10.61	A	synonymous_variant	LOW	ATAD3C	ENSG00000215915	Transcript	ENST00000378785	protein_coding	8/12		ENST00000378785.7:c.727C>A	ENSP00000368062.2:p.Arg243=	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|||||||	156,6	0.044	162	59,5	57,0	127,5	NA	0|1	0|1	1457166_C_A	NA	1457166	55,101,1,5	pakistan1_PS-9941-44_tumour
chr1	1457167		G	A	NA	PASS	SITE	55,106|1,5	NA	NA	179	2	93	37,37	126,138	52,53	3	NA	NA	NA	NA	NA	3.65	16	NA	NA	NA	NA	NA	NA	14.33	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|||||||	161,6	0.043	167	64,2	55,3	132,5	NA	1|0	1|0	1457166_C_A	NA	1457166	55,106,1,5	pakistan1_PS-9941-44_tumour
chr1	1460987		C	T	NA	PASS	SITE	12,65|2,2	NA	NA	82	1	93	37,20	165,143	60,60	57	NA	NA	NA	NA	NA	4.13	8	NA	NA	NA	NA	NA	NA	4.67	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||||||||||||||||||||||||||||||||||||||||||	77,4	0.043	81	32,1	32,1	65,2	NA	0/1	NA	NA	NA	NA	12,65,2,2	pakistan1_PS-9941-44_tumour
chr1	1462601		C	T	NA	PASS	SITE	155,87|4,1	NA	NA	255	1	93	37,37	125,110	56,53	20	NA	NA	NA	NA	NA	4.61	3	NA	NA	NA	NA	NA	NA	6.82	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|||||||	242,5	0.024	247	99,1	103,3	204,4	NA	0/1	NA	NA	NA	NA	155,87,4,1	pakistan1_PS-9941-44_tumour
chr1	1462875		G	A	NA	PASS	SITE	0,1|1,1	NA	NA	3	1	2	37,20	268,215	60,60	12	NA	NA	NA	NA	NA	4.61	5	NA	NA	NA	NA	NA	NA	4.17	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||||||||||	1,2	0.5	3	1,1	0,0	1,1	NA	0/1	NA	NA	NA	NA	0,1,1,1	pakistan1_PS-9941-44_tumour
chr1	1468566		G	A	NA	PASS	SITE	13,87|1,5	NA	NA	108	2	93	37,31	135,136	40,40	1	NA	NA	NA	NA	NA	4.61	19	NA	NA	NA	NA	NA	NA	10.4	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||||||||||	100,6	0.063	106	38,3	50,2	88,5	NA	0/1	NA	NA	NA	NA	13,87,1,5	pakistan1_PS-9941-44_tumour
chr1	1468593		G	A	NA	PASS	SITE	6,39|0,3	NA	NA	73	2	93	37,37	151,160	40,40	20	NA	NA	NA	NA	NA	7.3	9	NA	NA	NA	NA	NA	NA	6.71	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|||||||||||||||||||||||||||||||||||	45,3	0.086	48	20,1	20,2	40,3	NA	0/1	NA	NA	NA	NA	6,39,0,3	pakistan1_PS-9941-44_tumour
chr1	1474479		C	T	NA	PASS	SITE	0,0|0,0	NA	NA	1	1	31	0,37	0,150	60,60	19	NA	NA	NA	NA	NA	7.3	7	NA	NA	NA	NA	NA	NA	3.88	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|||||||||||||||||||||||||||||||||||	0,1	0.667	1	0,0	0,1	0,1	NA	0/1	NA	NA	NA	NA	0,0,1,0	pakistan1_PS-9941-44_tumour
chr1	1477486		G	A	NA	PASS	SITE	4,13|0,3	NA	NA	20	1	21	37,37	190,192	60,60	22	NA	NA	NA	NA	NA	4.13	14	NA	NA	NA	NA	NA	NA	8.35	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||||||||||	17,3	0.201	20	9,1	5,2	15,3	NA	0/1	NA	NA	NA	NA	4,13,0,3	pakistan1_PS-9941-44_tumour
chr1	1482715		T	C	NA	PASS	SITE	1,38|0,2	NA	NA	41	1	90	37,37	166,241	57,60	18	NA	NA	NA	NA	NA	4.31	3	NA	NA	NA	NA	NA	NA	3.85	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||||||||||	39,2	0.071	41	23,2	15,0	38,2	NA	0/1	NA	NA	NA	NA	1,38,0,2	pakistan1_PS-9941-44_tumour
chr1	1486686		C	T	NA	PASS	SITE	0,0|2,1	NA	NA	3	1	35	0,20	0,184	60,44	53	NA	NA	NA	NA	NA	7.3	8	NA	NA	NA	NA	NA	NA	7.42	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|||||||||||||||||||||||||||||||||||	0,3	0.75	3	0,0	0,2	0,2	NA	0/1	NA	NA	NA	NA	0,0,2,1	pakistan1_PS-9941-44_tumour
chr1	1489325		C	T	NA	PASS	SITE	17,128|1,2	NA	NA	158	2	93	37,20	135,139	54,60	51	NA	NA	NA	NA	NA	7.3	7	NA	NA	NA	NA	NA	NA	3.01	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||||||||||	145,3	0.022	148	59,1	66,1	130,2	NA	0/1	NA	NA	NA	NA	17,128,1,2	pakistan1_PS-9941-44_tumour