// Protocol buffer definitions for gnomAD v3 VEP records.

syntax = "proto3";

package annonars.gnomad.vep_gnomad3;

import "annonars/gnomad/vep_common.proto";

// Protocol buffer for the gnomAD-nuclear VEP predictions.
message Vep {
    // Allele of record.
    string allele = 1;
    // Consequence, e.g., `"missense_variant"`.
    string consequence = 2;
    // Impact, e.g., `"MODERATE"`.
    string impact = 3;
    // Gene symbol, e.g., `"PCSK9"`.
    string symbol = 4;
    // Gene ID, `e.g., "ENSG00000169174"`.
    string gene = 5;
    // Feature type, e.g., `"Transcript"`.
    string feature_type = 6;
    // Feature ID, e.g., `"ENST00000302118"`.
    string feature = 7;
    // Feature biotype, e.g., `"protein_coding"`.
    string feature_biotype = 8;
    // Ranked exon number, e.g., `"1/4"`.
    optional string exon = 9;
    // Ranked intron number, e.g., `"1/4"`.
    optional string intron = 10;
    // cDNA position, e.g., `"ENST00000302118.5:c.89C>G"`.
    optional string hgvsc = 11;
    // Protein position, e.g., `"ENSP00000302118.5:p.Thr30Arg"`.
    optional string hgvsp = 12;
    // cDNA position, e.g., `"89/1863"`.
    optional string cdna_position = 13;
    // CDS position, e.g., `"89/1863"`.
    optional string cds_position = 14;
    // Protein position, e.g., `"30/620"`.
    optional string protein_position = 15;
    // Amino acids, e.g., `"T/R"`.
    optional string amino_acids = 16;
    // Codons, e.g., `"gCg/gGg"`.
    optional string codons = 17;
    // TODO: actually is optional int32 allele_num = 18;
    // dbSNP ID, e.g., `"rs28942080"`.
    optional string dbsnp_id = 18;
    // Distance output of VEP.
    optional string distance = 19;
    // Strand, e.g., `"1"`.
    optional string strand = 20;
    // Variant class, e.g., `"SNV"`.
    optional string variant_class = 21;
    // Minimised output of VEP.
    optional string minimised = 22;
    // Symbol source, e.g., `"HGNC"`.
    optional string symbol_source = 23;
    // HGNC ID, e.g., `"HGNC:8706"`.
    optional string hgnc_id = 24;
    // Whether this is the canonical transcript.
    optional bool canonical = 25;
    // Transcript support level, e.g., `"1"`.
    optional int32 tsl = 26;
    // APPRIS annotation, e.g. `"P1"`.
    optional string appris = 27;
    // CCDS ID, e.g., `"CCDS30547.1"`.
    optional string ccds = 28;
    // Ensembl protein ID, e.g., `"ENSP00000302118"`.
    optional string ensp = 29;
    // SwissProt ID, e.g., `"P04114"`.
    optional string swissprot = 30;
    // TREMBL ID, e.g., `"Q5T4W7"`.
    optional string trembl = 31;
    // UniParc ID, e.g., `"UPI000002D4B2"`.
    optional string uniparc = 32;
    // Gene phenotype from VEP.
    optional string gene_pheno = 33;
    // SIFT prediction, e.g., `"tolerated(0.06)"`.
    optional annonars.gnomad.vep_common.Prediction sift = 34;
    // PolyPhen prediction, e.g., `"benign(0.001)"`.
    optional annonars.gnomad.vep_common.Prediction polyphen = 35;
    // Protein domains, e.g., `[["2p4e", "ENSP_mappings"], ["2qtw", "ENSP_mappings"]]`.
    repeated annonars.gnomad.vep_common.Domain domains = 36;
    // HGVS offset.
    optional string hgvs_offset = 37;
    // Motif name.
    optional string motif_name = 38;
    // Motif name.
    optional string motif_pos = 39;
    // "high inf pos" from VEP.
    optional string high_inf_pos = 40;
    // Motif score change.
    optional string motif_score_change = 41;
    // Loss of function prediction.
    optional string lof = 42;
    // Loss of function filter.
    optional string lof_filter = 43;
    // Loss of function flags.
    optional string lof_flags = 44;
    // Loss of function info.
    optional string lof_info = 45;
}