{"_id":"chr16:g.13947752C>T","_version":1,"chrom":"16","clingen":{"caid":"CA7910688"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"I","codon_degeneracy":0,"codonpos":2,"pos":719,"ref":"T","refcodon":"ACT"},"alphamissense":{"pred":"P","rankscore":0.76331,"score":0.7791},"alt":"T","altai_neandertal":["C","C"],"ancestral_allele":"C","appris":"principal1","bayesdel":{"add_af":{"pred":"D","rankscore":0.75302,"score":0.215003},"no_af":{"pred":"D","rankscore":0.7498,"score":0.071061}},"bstatistic":{"converted_rankscore":0.09725,"score":957.0},"cadd":{"phred":25.5,"raw_rankscore":0.70227,"raw_score":4.493814},"cds_strand":"+","chagyrskaya_neandertal":["C","C"],"chrom":"16","clinpred":{"pred":"D","rankscore":0.84301,"score":0.993483483791351},"dann":{"rankscore":0.97426,"score":0.9990271981399322},"denisova":["C","C"],"deogen2":{"pred":"D","rankscore":0.82491,"score":0.506949},"eigen":{"phred_coding":7.551429,"raw_coding":0.729436633885555,"raw_coding_rankscore":0.81564},"eigen-pc":{"phred_coding":7.73106,"raw_coding":0.698863357211229,"raw_coding_rankscore":0.82293},"ensembl":{"geneid":"ENSG00000175595","proteinid":"ENSP00000310520","transcriptid":"ENST00000311895"},"esm1b":{"pred":"D","rankscore":0.90727,"score":-13.343},"eve":{"class10_pred":"P","class20_pred":"P","class25_pred":"P","class30_pred":"P","class40_pred":"P","class50_pred":"P","class60_pred":"P","class70_pred":"P","class75_pred":"P","class80_pred":"P","class90_pred":"P","rankscore":0.98766,"score":0.9623876671013232},"exac":{"ac":1,"adj_ac":1,"adj_af":8.237e-6,"af":8.236e-6,"afr":{"ac":0,"af":0.0},"amr":{"ac":0,"af":0.0},"eas":{"ac":0,"af":0.0},"fin":{"ac":0,"af":0.0},"nfe":{"ac":1,"af":0.00001498},"sas":{"ac":0,"af":0.0}},"exac_nonpsych":{"ac":1,"adj_ac":1,"adj_af":0.00001102,"af":0.00001102,"afr":{"ac":0,"af":0.0},"amr":{"ac":0,"af":0.0},"eas":{"ac":0,"af":0.0},"fin":{"ac":0,"af":0.0},"nfe":{"ac":1,"af":0.00002373},"sas":{"ac":0,"af":0.0}},"exac_nontcga":{"ac":1,"adj_ac":1,"adj_af":9.416e-6,"af":9.415e-6,"afr":{"ac":0,"af":0.0},"amr":{"ac":0,"af":0.0},"eas":{"ac":0,"af":0.0},"fin":{"ac":0,"af":0.0},"nfe":{"ac":1,"af":0.0000184},"sas":{"ac":0,"af":0.0}},"fathmm":{"converted_rankscore":0.21865,"pred":"T","score":1.98},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.72204,"coding_score":0.97016},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.54876,"coding_score":0.526376},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.12157,"score":0.546412},"h1-hesc":{"confidence_value":0,"rankscore":0.50148,"score":0.65145},"huvec":{"confidence_value":0,"rankscore":0.53088,"score":0.635551},"integrated":{"confidence_value":0,"rankscore":0.46895,"score":0.6512}},"gencode_basic":"Y","genename":"ERCC4","genocanyon":{"rankscore":0.74766,"score":0.999999939628365},"gerp":{"91_mammals":{"rankscore":0.55512,"score":3.04}},"gerp++":{"nr":5.58,"rs":5.58,"rs_rankscore":0.84361},"gmvp":{"rankscore":0.77279,"score":0.7732912466650341},"hg18":{"end":13949110,"start":13949110},"hg19":{"end":14041609,"start":14041609},"hg38":{"end":13947752,"start":13947752},"hgvsc":"c.2156C>T","hgvsp":["p.Thr719Ile","p.T719I"],"interpro":{"domain":"ERCC4 domain|ERCC4 domain"},"list-s2":{"pred":"D","rankscore":0.82551,"score":0.954105},"lrt":{"converted_rankscore":0.8433,"omega":0.094625,"pred":"D","score":1e-6},"m-cap":{"pred":"D","rankscore":0.54416,"score":0.032652},"metalr":{"pred":"T","rankscore":0.47111,"score":0.1465},"metarnn":{"pred":"D","rankscore":0.84225,"score":0.8504952},"metasvm":{"pred":"T","rankscore":0.45027,"score":-0.9238},"mpc":{"rankscore":0.44323,"score":0.443996096836},"mutationassessor":{"pred":"M","rankscore":0.89398,"score":3.22},"mutationtaster":{"aae":"T719I","converted_rankscore":0.81001,"model":"simple_aae","pred":"D","score":1.0},"mutformer":{"rankscore":0.72422,"score":0.18432023},"mutpred":{"aa_change":"T719I","accession":"Q92889","pred":{"mechanism":"Gain of sheet","p_val":0.0149},"rankscore":0.69564,"score":0.572},"mvp":{"rankscore":0.7454,"score":0.747678149226},"phactboost":{"rankscore":0.8619,"score":0.983484527642277},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.41813,"score":0.876},"470way_mammalian":{"rankscore":0.35428,"score":0.999}},"phylop":{"100way_vertebrate":{"rankscore":0.60422,"score":4.547},"17way_primate":{"rankscore":0.4025,"score":0.599},"470way_mammalian":{"rankscore":0.41039,"score":3.997}},"polyphen2":{"hdiv":{"pred":"D","rankscore":0.7322,"score":0.998},"hvar":{"pred":"D","rankscore":0.72923,"score":0.973}},"primateai":{"pred":"T","rankscore":0.64473,"score":0.681428253651},"provean":{"converted_rankscore":0.77637,"pred":"D","score":-4.44},"ref":"C","reliability_index":10,"revel":{"rankscore":0.64008,"score":0.318},"rsid":"rs779096061","sift":{"converted_rankscore":0.7849,"pred":"D","score":0.001},"sift4g":{"converted_rankscore":0.79402,"pred":"D","score":0.002},"siphy_29way":{"logodds_rankscore":0.91089,"logodds_score":18.5707,"pi":{"a":0.0,"c":1.0,"g":0.0,"t":0.0}},"tsl":1,"uniprot":{"acc":"Q92889","entry":"XPF_HUMAN"},"varity":{"er":{"rankscore":0.92086,"score":0.85863286},"er_loo":{"rankscore":0.92086,"score":0.85863286},"r":{"rankscore":0.94584,"score":0.93346256},"r_loo":{"rankscore":0.94584,"score":0.93346256}},"vep_canonical":"YES","vest4":{"rankscore":0.90476,"score":0.904},"vindijia_neandertal":["C","C"]},"dbsnp":{"_license":"http://bit.ly/2AqoLOc","alleles":[{"allele":"C","freq":{"dbgap_popfreq":1.0,"gnomad":1.0,"topmed":1.0}},{"allele":"A","freq":{"dbgap_popfreq":0.0,"gnomad":0.0,"topmed":0.0}}],"alt":"T","chrom":"16","dbsnp_build":156,"gene":{"geneid":2072,"is_pseudo":false,"name":"ERCC excision repair 4, endonuclease catalytic subunit","rnas":[{"codon_aligned_transcript_change":{"deleted_sequence":"ACT","inserted_sequence":"ACT","position":2166,"seq_id":"NM_005236.3"},"hgvs":"NM_005236.3:c.2156=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":718,"seq_id":"NP_005227.1"}}},"protein_product":{"refseq":"NP_005227.1"},"refseq":"NM_005236.3","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACT","inserted_sequence":"ACT","position":2304,"seq_id":"XM_011522424.4"},"hgvs":"XM_011522424.4:c.2294=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":764,"seq_id":"XP_011520726.1"}}},"protein_product":{"refseq":"XP_011520726.1"},"refseq":"XM_011522424.4","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACT","inserted_sequence":"ACT","position":1141,"seq_id":"XM_011522427.2"},"hgvs":"XM_011522427.2:c.806=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":268,"seq_id":"XP_011520729.1"}}},"protein_product":{"refseq":"XP_011520729.1"},"refseq":"XM_011522427.2","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]},{"codon_aligned_transcript_change":{"deleted_sequence":"ACT","inserted_sequence":"ACT","position":1510,"seq_id":"XM_047433774.1"},"hgvs":"XM_047433774.1:c.1367=","protein":{"variant":{"spdi":{"deleted_sequence":"T","inserted_sequence":"T","position":455,"seq_id":"XP_047289730.1"}}},"protein_product":{"refseq":"XP_047289730.1"},"refseq":"XM_047433774.1","so":[{"accession":"SO:0001580","name":"coding_sequence_variant"}]}],"strand":"+","symbol":"ERCC4"},"hg38":{"end":13947752,"start":13947752},"ref":"C","rsid":"rs779096061","vartype":"snv"},"gnomad_exome":{"_license":"http://bit.ly/2I1cl1I","ac":{"ac":1,"ac_afr":0,"ac_afr_female":0,"ac_afr_male":0,"ac_amr":0,"ac_amr_female":0,"ac_amr_male":0,"ac_asj":0,"ac_asj_female":0,"ac_asj_male":0,"ac_eas":0,"ac_eas_female":0,"ac_eas_jpn":0,"ac_eas_kor":0,"ac_eas_male":0,"ac_eas_oea":0,"ac_female":0,"ac_fin":0,"ac_fin_female":0,"ac_fin_male":0,"ac_male":1,"ac_nfe":1,"ac_nfe_bgr":0,"ac_nfe_est":0,"ac_nfe_female":0,"ac_nfe_male":1,"ac_nfe_nwe":0,"ac_nfe_onf":0,"ac_nfe_seu":1,"ac_nfe_swe":0,"ac_oth":0,"ac_oth_female":0,"ac_oth_male":0,"ac_sas":0,"ac_sas_female":0,"ac_sas_male":0},"af":{"af":3.97703e-6,"af_afr":0.0,"af_afr_female":0.0,"af_afr_male":0.0,"af_amr":0.0,"af_amr_female":0.0,"af_amr_male":0.0,"af_asj":0.0,"af_asj_female":0.0,"af_asj_male":0.0,"af_eas":0.0,"af_eas_female":0.0,"af_eas_jpn":0.0,"af_eas_kor":0.0,"af_eas_male":0.0,"af_eas_oea":0.0,"af_female":0.0,"af_fin":0.0,"af_fin_female":0.0,"af_fin_male":0.0,"af_male":7.359e-6,"af_nfe":8.79291e-6,"af_nfe_bgr":0.0,"af_nfe_est":0.0,"af_nfe_female":0.0,"af_nfe_male":0.0000157277,"af_nfe_nwe":0.0,"af_nfe_onf":0.0,"af_nfe_seu":0.0000869414,"af_nfe_swe":0.0,"af_oth":0.0,"af_oth_female":0.0,"af_oth_male":0.0,"af_sas":0.0,"af_sas_female":0.0,"af_sas_male":0.0},"alleles":"T","alt":"T","an":{"an":251444,"an_afr":16256,"an_afr_female":10070,"an_afr_male":6186,"an_amr":34592,"an_amr_female":20270,"an_amr_male":14322,"an_asj":10076,"an_asj_female":4896,"an_asj_male":5180,"an_eas":18390,"an_eas_female":9328,"an_eas_jpn":152,"an_eas_kor":3814,"an_eas_male":9062,"an_eas_oea":14424,"an_female":115556,"an_fin":21648,"an_fin_female":10374,"an_fin_male":11274,"an_male":135888,"an_nfe":113728,"an_nfe_bgr":2670,"an_nfe_est":242,"an_nfe_female":50146,"an_nfe_male":63582,"an_nfe_nwe":42200,"an_nfe_onf":30982,"an_nfe_seu":11502,"an_nfe_swe":26132,"an_oth":6138,"an_oth_female":2928,"an_oth_male":3210,"an_sas":30616,"an_sas_female":7544,"an_sas_male":23072},"baseqranksum":-3.372,"chrom":"16","clippingranksum":-0.114,"dp":11853312,"fs":7.09,"hom":{"hom":0,"hom_afr":0,"hom_afr_female":0,"hom_afr_male":0,"hom_amr":0,"hom_amr_female":0,"hom_amr_male":0,"hom_asj":0,"hom_asj_female":0,"hom_asj_male":0,"hom_eas":0,"hom_eas_female":0,"hom_eas_jpn":0,"hom_eas_kor":0,"hom_eas_male":0,"hom_eas_oea":0,"hom_female":0,"hom_fin":0,"hom_fin_female":0,"hom_fin_male":0,"hom_male":0,"hom_nfe":0,"hom_nfe_bgr":0,"hom_nfe_est":0,"hom_nfe_female":0,"hom_nfe_male":0,"hom_nfe_nwe":0,"hom_nfe_onf":0,"hom_nfe_seu":0,"hom_nfe_swe":0,"hom_oth":0,"hom_oth_female":0,"hom_oth_male":0,"hom_sas":0,"hom_sas_female":0,"hom_sas_male":0},"inbreedingcoeff":0.0,"mq":{"mq":59.44,"mqranksum":0.373},"pab_max":0.635308,"pos":13947752,"qd":13.36,"readposranksum":1.11,"ref":"C","rf":0.920717,"rsid":"rs779096061","sor":1.135,"type":"snp","vqslod":-0.2952,"vqsr_culprit":"FS"},"hg38":{"end":13947752,"start":13947752},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"6761","position":"2165"},"cds":{"length":"2751","position":"2156"},"effect":"missense_variant","feature_id":"NM_005236.2","feature_type":"transcript","gene_id":"ERCC4","genename":"ERCC4","hgvs_c":"c.2156C>T","hgvs_p":"p.Thr719Ile","protein":{"length":"916","position":"719"},"putative_impact":"MODERATE","rank":"11","total":"11","transcript_biotype":"protein_coding"}},"vcf":{"alt":"T","position":"13947752","ref":"C"}}