{"_id":"chr16:g.13948054A>C","_version":1,"chrom":"16","clingen":{"caid":"CA394823928"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"Q","codon_degeneracy":0,"codonpos":1,"pos":820,"ref":"K","refcodon":"AAG"},"alphamissense":{"pred":"B","rankscore":0.14062,"score":0.0931},"alt":"C","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":"principal1","bayesdel":{"add_af":{"pred":"T","rankscore":0.31056,"score":-0.132728},"no_af":{"pred":"T","rankscore":0.30114,"score":-0.428431}},"bstatistic":{"converted_rankscore":0.09725,"score":957.0},"cadd":{"phred":18.48,"raw_rankscore":0.30579,"raw_score":2.382152},"cds_strand":"+","chagyrskaya_neandertal":["A","A"],"chrom":"16","clinpred":{"pred":"D","rankscore":0.38561,"score":0.652299642562866},"dann":{"rankscore":0.39193,"score":0.982093447260342},"denisova":["A","A"],"deogen2":{"pred":"T","rankscore":0.43438,"score":0.115637},"eigen":{"phred_coding":1.275862,"raw_coding":-0.45053513773001,"raw_coding_rankscore":0.23722},"eigen-pc":{"phred_coding":1.586794,"raw_coding":-0.28910756043058,"raw_coding_rankscore":0.28457},"ensembl":{"geneid":"ENSG00000175595","proteinid":"ENSP00000310520","transcriptid":"ENST00000311895"},"esm1b":{"pred":"T","rankscore":0.35892,"score":-4.914},"eve":{"class10_pred":"U","class20_pred":"B","class25_pred":"B","class30_pred":"B","class40_pred":"B","class50_pred":"B","class60_pred":"B","class70_pred":"B","class75_pred":"B","class80_pred":"B","class90_pred":"B","rankscore":0.08173,"score":0.10445903834356016},"fathmm":{"converted_rankscore":0.58755,"pred":"T","score":0.3},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.40317,"coding_score":0.80761},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.23122,"coding_score":0.118197},"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":0.32258,"score":0.990759597297777},"gerp":{"91_mammals":{"rankscore":0.38685,"score":1.92}},"gerp++":{"nr":6.16,"rs":3.84,"rs_rankscore":0.43422},"gmvp":{"rankscore":0.26582,"score":0.26669858425227677},"hg18":{"end":13949412,"start":13949412},"hg19":{"end":14041911,"start":14041911},"hg38":{"end":13948054,"start":13948054},"hgvsc":"c.2458A>C","hgvsp":["p.K820Q","p.Lys820Gln"],"list-s2":{"pred":"D","rankscore":0.57574,"score":0.870713},"lrt":{"converted_rankscore":0.62929,"omega":0.107297,"pred":"D","score":7e-6},"m-cap":{"pred":"T","rankscore":0.42684,"score":0.020152},"metalr":{"pred":"T","rankscore":0.4049,"score":0.1136},"metarnn":{"pred":"T","rankscore":0.2233,"score":0.11815068},"metasvm":{"pred":"T","rankscore":0.39644,"score":-0.9575},"mpc":{"rankscore":0.09938,"score":0.0880244292771},"mutationassessor":{"pred":"N","rankscore":0.15482,"score":0.595},"mutationtaster":{"aae":"K820Q","converted_rankscore":0.33339,"model":"simple_aae","pred":"D","score":0.692397},"mutformer":{"rankscore":0.47278,"score":0.01646992},"mutpred":{"aa_change":"K820Q","accession":"Q92889","pred":{"mechanism":"Loss of ubiquitination at K820","p_val":0.0067},"rankscore":0.21735,"score":0.269},"mvp":{"rankscore":0.8249,"score":0.82654850784},"phactboost":{"rankscore":0.34067,"score":0.0348720760843997},"phastcons":{"100way_vertebrate":{"rankscore":0.40164,"score":0.997},"17way_primate":{"rankscore":0.54022,"score":0.969},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.57456,"score":4.095},"17way_primate":{"rankscore":0.94297,"score":0.756},"470way_mammalian":{"rankscore":0.51257,"score":5.927}},"polyphen2":{"hdiv":{"pred":"B","rankscore":0.15093,"score":0.009},"hvar":{"pred":"B","rankscore":0.19346,"score":0.021}},"primateai":{"pred":"T","rankscore":0.17765,"score":0.348923802376},"provean":{"converted_rankscore":0.19085,"pred":"N","score":-0.66},"ref":"A","reliability_index":10,"revel":{"rankscore":0.09825,"score":0.038},"sift":{"converted_rankscore":0.28271,"pred":"T","score":0.117},"sift4g":{"converted_rankscore":0.29346,"pred":"T","score":0.181},"siphy_29way":{"logodds_rankscore":0.61347,"logodds_score":13.5776,"pi":{"a":0.4689,"c":0.5311,"g":0.0,"t":0.0}},"tsl":1,"uniprot":{"acc":"Q92889","entry":"XPF_HUMAN"},"varity":{"er":{"rankscore":0.21746,"score":0.09229994},"er_loo":{"rankscore":0.21745,"score":0.09229994},"r":{"rankscore":0.62867,"score":0.43175706},"r_loo":{"rankscore":0.62867,"score":0.43175706}},"vep_canonical":"YES","vest4":{"rankscore":0.14763,"score":0.146},"vindijia_neandertal":["A","A"]},"hg38":{"end":13948054,"start":13948054},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":{"cdna":{"length":"6761","position":"2467"},"cds":{"length":"2751","position":"2458"},"effect":"missense_variant","feature_id":"NM_005236.2","feature_type":"transcript","gene_id":"ERCC4","genename":"ERCC4","hgvs_c":"c.2458A>C","hgvs_p":"p.Lys820Gln","protein":{"length":"916","position":"820"},"putative_impact":"MODERATE","rank":"11","total":"11","transcript_biotype":"protein_coding"}},"vcf":{"alt":"C","position":"13948054","ref":"A"}}