TogoVar Downloadable data Last Updated: 2024/2/28 See https://grch38.togovar.org/doc/datasets about the datasets. ------------------------------------------------------------------------------------------------------------------------ 1. Allele and genotype frequency Key value that identifies one record: tgv_id Variable name Description ------------------------------------------------------------------------------------------------------------------------ tgv_id :Togovar ID rs :dbSNP rs number variant_type :variant type chr :chromosome number position_grch38 :chromosomal position on GRCh38 ref :reference allele alt :alternative allele symbol :HGNC gene symbol jga_ngs_allele_alt :number of alternative alleles in JGA-NGS jga_ngs_allele_total :total number of alleles in JGA-NGS jga_ngs_alt_allele_freq :alternative allele frequency in JGA-NGS jga_ngs_qc_status :variant calling quality filter status for JGA-NGS variant jga_snp_allele_alt :number of alternative alleles in JGA-SNP jga_snp_allele_total :total number of alleles in JGA-SNP jga_snp_alt_allele_freq :alternative allele frequency in JGA-SNP jga_snp_genotype_alt_alt :number of homozygous alternative genotypes in JGA-SNP jga_snp_genotype_ref_alt :number of heterozygous genotypes in JGA-SNP jga_snp_genotype_ref_ref :number of homozygous reference genotypes in JGA-SNP jga_snp_qc_status :variant calling quality filter status for JGA-SNP variant tommo_allele_alt :number of alternative alleles in ToMMo tommo_allele_total :total number of alleles in ToMMo tommo_alt_allele_freq :alternative allele frequency in ToMMo tommo_qc_status :variant calling quality filter status for ToMMo variant gem_j_wga_total_allele_alt :total number of alternative alleles in GEM-J WGA gem_j_wga_total_allele_total :total number of alleles in GEM-J WGA gem_j_wga_total_alt_allele_freq :alternative allele frequency in GEM-J WGA gem_j_wga_total_qc_status :variant calling quality filter status for GEM-J WGA variant gnomad_genomes_total_allele_alt :total number of alternative alleles in gnomAD genomes gnomad_genomes_total_allele_total :total number of alleles in gnomAD genomes gnomad_genomes_total_alt_allele_freq :alternative allele frequency in gnomAD genomes gnomad_genomes_total_qc_status :variant calling quality filter status for gnomAD genomes variant gnomad_exomes_total_allele_alt :total number of alternative alleles in gnomAD exomes gnomad_exomes_total_allele_total :total number of alleles in gnomAD exomes gnomad_exomes_total_alt_allele_freq :alternative allele frequency in gnomAD exomes gnomad_exomes_total_qc_status :variant calling quality filter status for gnomAD exomes variant 2. Molecular annotation Key values that identify one record: tgv_id and transcript_id Variable name Description ------------------------------------------------------------------------------------------------------------------------ tgv_id :Togovar ID rs :dbSNP rs number chr :chromosome number position_grch38 :chromosomal position on GRCh38 ref :reference allele alt :alternative allele symbol :HGNC gene symbol transcript_id :Ensembl transcript ID consequence :molecular consequence predicted by Variant Effective Predictor sift_qualitative_prediction :qualitative prediction by SIFT sift_score :SIFT score polyphen2_qualitative_prediction :qualitative prediction by PolyPhen2 polyphen2_score :PolyPhen2 score alphamissense_prediction :variant classification by AlphaMissense: 'Likely pathogenic', 'Likely benign', 'ambiguous'. Details: https://asia.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#alphamissense alphamissense_score :a continuous score between 0 and 1 predicted by AlphaMissense