{"_id":"chr16:g.13947838A>C","_version":1,"chrom":"16","clingen":{"caid":"CA394822683"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"L","codon_degeneracy":0,"codonpos":1,"pos":748,"ref":"M","refcodon":"ATG"},"alphamissense":{"pred":"P","rankscore":0.69559,"score":0.6165},"alt":"C","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.59303,"score":0.0575388},"no_af":{"pred":"T","rankscore":0.58789,"score":-0.155126}},"bstatistic":{"converted_rankscore":0.09725,"score":957.0},"cadd":{"phred":25.2,"raw_rankscore":0.682,"raw_score":4.409649},"cds_strand":"+","chagyrskaya_neandertal":["A","A"],"chrom":"16","clinpred":{"pred":"D","rankscore":0.76962,"score":0.986174619663092},"dann":{"rankscore":0.444,"score":0.9866558510469072},"denisova":["A","A"],"deogen2":{"pred":"T","rankscore":0.73163,"score":0.366376},"eigen":{"phred_coding":7.954477,"raw_coding":0.754479461479082,"raw_coding_rankscore":0.83197},"eigen-pc":{"phred_coding":9.412456,"raw_coding":0.774586592255151,"raw_coding_rankscore":0.87978},"ensembl":{"geneid":"ENSG00000175595","proteinid":"ENSP00000310520","transcriptid":"ENST00000311895"},"esm1b":{"pred":"D","rankscore":0.71566,"score":-9.614},"eve":{"class10_pred":"U","class20_pred":"U","class25_pred":"U","class30_pred":"U","class40_pred":"U","class50_pred":"U","class60_pred":"U","class70_pred":"U","class75_pred":"U","class80_pred":"P","class90_pred":"P","rankscore":0.70439,"score":0.6345451860656965},"fathmm":{"converted_rankscore":0.12371,"pred":"T","score":2.68},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.93429,"coding_score":0.99249},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.82238,"coding_score":0.888854},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.12157,"score":0.546412},"h1-hesc":{"confidence_value":0,"rankscore":0.6058,"score":0.670488},"huvec":{"confidence_value":0,"rankscore":0.53088,"score":0.635551},"integrated":{"confidence_value":0,"rankscore":0.31514,"score":0.562547}},"gencode_basic":"Y","genename":"ERCC4","genocanyon":{"rankscore":0.74766,"score":0.999999999684514},"gerp++":{"nr":5.79,"rs":5.79,"rs_rankscore":0.91751},"gmvp":{"rankscore":0.75217,"score":0.7527074060320381},"hg18":{"end":13949196,"start":13949196},"hg19":{"end":14041695,"start":14041695},"hg38":{"end":13947838,"start":13947838},"hgvsc":"c.2242A>C","hgvsp":["p.Met748Leu","p.M748L"],"interpro":{"domain":"ERCC4 domain|ERCC4 domain"},"list-s2":{"pred":"D","rankscore":0.60664,"score":0.884012},"lrt":{"converted_rankscore":0.8433,"omega":0.0,"pred":"D","score":0.0},"m-cap":{"pred":"D","rankscore":0.55449,"score":0.034107},"metalr":{"pred":"T","rankscore":0.31163,"score":0.0782},"metarnn":{"pred":"D","rankscore":0.78121,"score":0.7843663},"metasvm":{"pred":"T","rankscore":0.01703,"score":-1.1317},"mpc":{"rankscore":0.43385,"score":0.432008363034},"mutationassessor":{"pred":"M","rankscore":0.54099,"score":1.995},"mutationtaster":{"aae":"M748L","converted_rankscore":0.81001,"model":"simple_aae","pred":"D","score":1.0},"mutformer":{"rankscore":0.69697,"score":0.1375065},"mutpred":{"aa_change":"M748L","accession":"Q92889","pred":{"mechanism":"Loss of catalytic residue at M748","p_val":0.02},"rankscore":0.74652,"score":0.613},"mvp":{"rankscore":0.80624,"score":0.808047262888},"phactboost":{"rankscore":0.91545,"score":0.995749515550191},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.79791,"score":0.997},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.90993,"score":8.688},"17way_primate":{"rankscore":0.94297,"score":0.756},"470way_mammalian":{"rankscore":0.871,"score":11.142}},"polyphen2":{"hdiv":{"pred":"D","rankscore":0.77913,"score":0.999},"hvar":{"pred":"D","rankscore":0.84481,"score":0.996}},"primateai":{"pred":"T","rankscore":0.47573,"score":0.562171041965},"provean":{"converted_rankscore":0.5971,"pred":"D","score":-2.83},"ref":"A","reliability_index":10,"revel":{"rankscore":0.70603,"score":0.39},"sift":{"converted_rankscore":0.91255,"pred":"D","score":0.0},"sift4g":{"converted_rankscore":0.92824,"pred":"D","score":0.0},"siphy_29way":{"logodds_rankscore":0.73793,"logodds_score":15.3166,"pi":{"a":1.0,"c":0.0,"g":0.0,"t":0.0}},"tsl":1,"uniprot":{"acc":"Q92889","entry":"XPF_HUMAN"},"varity":{"er":{"rankscore":0.93008,"score":0.87205076},"er_loo":{"rankscore":0.93008,"score":0.87205076},"r":{"rankscore":0.88655,"score":0.867381},"r_loo":{"rankscore":0.88657,"score":0.867381}},"vep_canonical":"YES","vest4":{"rankscore":0.59223,"score":0.569},"vindijia_neandertal":["A","A"]},"gnomad_genome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":1,"ac_afr":0,"ac_afr_xx":0,"ac_afr_xy":0,"ac_ami":0,"ac_ami_xx":0,"ac_ami_xy":0,"ac_amr":0,"ac_amr_xx":0,"ac_amr_xy":0,"ac_asj":0,"ac_asj_xx":0,"ac_asj_xy":0,"ac_eas":0,"ac_eas_xx":0,"ac_eas_xy":0,"ac_fin":0,"ac_fin_xx":0,"ac_fin_xy":0,"ac_mid":0,"ac_mid_xx":0,"ac_mid_xy":0,"ac_nfe":0,"ac_nfe_xx":0,"ac_nfe_xy":0,"ac_oth":0,"ac_oth_xx":0,"ac_oth_xy":0,"ac_sas":1,"ac_sas_xx":0,"ac_sas_xy":1,"ac_xx":0,"ac_xy":1},"af":{"af":6.57194e-6,"af_afr":0.0,"af_afr_xx":0.0,"af_afr_xy":0.0,"af_ami":0.0,"af_ami_xx":0.0,"af_ami_xy":0.0,"af_amr":0.0,"af_amr_xx":0.0,"af_amr_xy":0.0,"af_asj":0.0,"af_asj_xx":0.0,"af_asj_xy":0.0,"af_eas":0.0,"af_eas_xx":0.0,"af_eas_xy":0.0,"af_fin":0.0,"af_fin_xx":0.0,"af_fin_xy":0.0,"af_mid":0.0,"af_mid_xx":0.0,"af_mid_xy":0.0,"af_nfe":0.0,"af_nfe_xx":0.0,"af_nfe_xy":0.0,"af_oth":0.0,"af_oth_xx":0.0,"af_oth_xy":0.0,"af_sas":0.000207125,"af_sas_xx":0.0,"af_sas_xy":0.000272926,"af_xx":0.0,"af_xy":0.0000134517},"alleles":"C","alt":"C","an":{"an":152162,"an_afr":41438,"an_afr_xx":22146,"an_afr_xy":19292,"an_ami":912,"an_ami_xx":470,"an_ami_xy":442,"an_amr":15270,"an_amr_xx":6782,"an_amr_xy":8488,"an_asj":3470,"an_asj_xx":1866,"an_asj_xy":1604,"an_eas":5196,"an_eas_xx":2278,"an_eas_xy":2918,"an_fin":10608,"an_fin_xx":2568,"an_fin_xy":8040,"an_mid":316,"an_mid_xx":164,"an_mid_xy":152,"an_nfe":68032,"an_nfe_xx":39352,"an_nfe_xy":28680,"an_oth":2092,"an_oth_xx":1032,"an_oth_xy":1060,"an_sas":4828,"an_sas_xx":1164,"an_sas_xy":3664,"an_xx":77822,"an_xy":74340},"as_fs":0.521554,"as_mq":{"as_mq":59.9184,"as_mqranksum":0.011},"as_pab_max":0.434993,"as_qd":14.2885,"as_readposranksum":0.893,"as_sor":0.764262,"as_vqslod":1.3025,"chrom":"16","hom":{"hom":0,"hom_afr":0,"hom_afr_xx":0,"hom_afr_xy":0,"hom_ami":0,"hom_ami_xx":0,"hom_ami_xy":0,"hom_amr":0,"hom_amr_xx":0,"hom_amr_xy":0,"hom_asj":0,"hom_asj_xx":0,"hom_asj_xy":0,"hom_eas":0,"hom_eas_xx":0,"hom_eas_xy":0,"hom_fin":0,"hom_fin_xx":0,"hom_fin_xy":0,"hom_mid":0,"hom_mid_xx":0,"hom_mid_xy":0,"hom_nfe":0,"hom_nfe_xx":0,"hom_nfe_xy":0,"hom_oth":0,"hom_oth_xx":0,"hom_oth_xy":0,"hom_sas":0,"hom_sas_xx":0,"hom_sas_xy":0,"hom_xx":0,"hom_xy":0},"inbreedingcoeff":-6.55651e-6,"pos":13947838,"ref":"A","type":"snp"},"hg38":{"end":13947838,"start":13947838},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"6761","position":"2251"},"cds":{"length":"2751","position":"2242"},"effect":"missense_variant","feature_id":"NM_005236.2","feature_type":"transcript","gene_id":"ERCC4","genename":"ERCC4","hgvs_c":"c.2242A>C","hgvs_p":"p.Met748Leu","protein":{"length":"916","position":"748"},"putative_impact":"MODERATE","rank":"11","total":"11","transcript_biotype":"protein_coding"}},"vcf":{"alt":"C","position":"13947838","ref":"A"}}