{"_id":"chr10:g.94298382C>T","_version":1,"chrom":"10","clingen":{"caid":"CA377641660"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"F","codon_degeneracy":[0,0,0],"codonpos":[2,2,2],"pos":[1724,1416,1416],"ref":"S","refcodon":["TCC","TCC","TCC"]},"alphamissense":{"pred":["B","B"],"rankscore":0.23325,"score":[0.1158,0.1056]},"alt":"T","altai_neandertal":["C","C"],"ancestral_allele":"C","appris":["principal3","alternative2","alternative2"],"bayesdel":{"add_af":{"pred":"T","rankscore":0.133,"score":-0.256613},"no_af":{"pred":"T","rankscore":0.1228,"score":-0.606383}},"bstatistic":{"converted_rankscore":0.84213,"score":372.0},"cadd":{"phred":22.2,"raw_rankscore":0.46062,"raw_score":3.342355},"cds_strand":["+","+","+"],"chagyrskaya_neandertal":["C","C"],"chrom":"10","clinpred":{"pred":"T","rankscore":0.27924,"score":0.373301655054092},"dann":{"rankscore":0.41531,"score":0.9844279520447967},"denisova":["C","C"],"deogen2":{"pred":"T","rankscore":0.54998,"score":0.194265},"eigen":{"phred_coding":1.957795,"raw_coding":-0.171512053002915,"raw_coding_rankscore":0.34324},"eigen-pc":{"phred_coding":2.260442,"raw_coding":-0.0296785125394629,"raw_coding_rankscore":0.3838},"ensembl":{"geneid":["ENSG00000138193","ENSG00000138193","ENSG00000138193"],"proteinid":["ENSP00000360431","ENSP00000360438","ENSP00000360426"],"transcriptid":["ENST00000371380","ENST00000371385","ENST00000371375"]},"esm1b":{"pred":["T","T","T"],"rankscore":0.39794,"score":[-5.249,-5.285,-5.285]},"eve":{"class10_pred":"U","class20_pred":"U","class25_pred":"U","class30_pred":"U","class40_pred":"U","class50_pred":"U","class60_pred":"U","class70_pred":"B","class75_pred":"B","class80_pred":"B","class90_pred":"B","rankscore":0.38411,"score":0.28789802503408035},"fathmm":{"converted_rankscore":0.26588,"pred":["T","T","T"],"score":[1.72,1.73,1.73]},"fathmm-mkl":{"coding_group":"AEFDBI","coding_pred":"D","coding_rankscore":0.38761,"coding_score":0.78535},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.3216,"coding_score":0.19453},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.26702,"score":0.573888},"h1-hesc":{"confidence_value":0,"rankscore":0.23631,"score":0.573888},"huvec":{"confidence_value":0,"rankscore":0.1498,"score":0.542086},"integrated":{"confidence_value":0,"rankscore":0.14033,"score":0.487112}},"gencode_basic":["Y","Y","Y"],"genename":["PLCE1","PLCE1","PLCE1"],"genocanyon":{"rankscore":0.14086,"score":0.0330550196858255},"gerp":{"91_mammals":{"rankscore":0.89747,"score":4.98}},"gerp++":{"nr":5.6,"rs":4.66,"rs_rankscore":0.57857},"gmvp":{"rankscore":0.50856,"score":0.5093497612226563},"hg18":{"end":96048129,"start":96048129},"hg19":{"end":96058139,"start":96058139},"hg38":{"end":94298382,"start":94298382},"hgvsc":["c.4247C>T","c.5171C>T"],"hgvsp":["p.S1724F","p.Ser1724Phe","p.Ser1416Phe","p.S1416F"],"list-s2":{"pred":["T","T"],"rankscore":0.31399,"score":[0.70393,0.70393]},"lrt":{"converted_rankscore":0.22792,"omega":0.447017,"pred":"N","score":0.053624},"m-cap":{"pred":"T","rankscore":0.16052,"score":0.006135},"metalr":{"pred":"T","rankscore":0.19316,"score":0.045},"metarnn":{"pred":["T","T","T"],"rankscore":0.04123,"score":[0.04770291,0.04770291,0.04770291]},"metasvm":{"pred":"T","rankscore":0.03274,"score":-1.1077},"mpc":{"rankscore":0.49436,"score":0.515258437671},"mutationassessor":{"pred":"N","rankscore":0.17993,"score":0.695},"mutationtaster":{"aae":["S1724F","S1416F","S1724F","S1416F"],"converted_rankscore":0.28369,"model":["simple_aae","simple_aae","simple_aae","simple_aae"],"pred":["N","N","N","N"],"score":[0.886845,0.860049,0.886845,0.860049]},"mutformer":{"rankscore":0.63983,"score":0.07637624},"mutpred":{"aa_change":"S1724F","accession":"Q9P212","pred":{"mechanism":"Gain of helix","p_val":0.0199},"rankscore":0.25881,"score":0.295},"mvp":{"rankscore":0.36766,"score":[0.371531589858,0.371531589858,0.371531589858]},"phactboost":{"rankscore":0.21522,"score":0.00728007397072391},"phastcons":{"100way_vertebrate":{"rankscore":0.26925,"score":0.496},"17way_primate":{"rankscore":0.60418,"score":0.984},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.43929,"score":2.374},"17way_primate":{"rankscore":0.4025,"score":0.599},"470way_mammalian":{"rankscore":0.40251,"score":3.883}},"polyphen2":{"hdiv":{"pred":["B","P","P"],"rankscore":0.51611,"score":[0.001,0.928,0.928]},"hvar":{"pred":["B","P","P"],"rankscore":0.46748,"score":[0.001,0.469,0.469]}},"primateai":{"pred":"T","rankscore":0.27943,"score":0.420783877373},"provean":{"converted_rankscore":0.60665,"pred":["N","D","D"],"score":[-2.41,-2.89,-2.89]},"ref":"C","reliability_index":10,"revel":{"rankscore":0.06676,"score":[0.029,0.029,0.029]},"sift":{"converted_rankscore":0.28148,"pred":["T","T","T"],"score":[0.118,0.126,0.126]},"sift4g":{"converted_rankscore":0.4553,"pred":["T","T","T"],"score":[0.112,0.061,0.061]},"siphy_29way":{"logodds_rankscore":0.56513,"logodds_score":12.7209,"pi":{"a":0.0,"c":0.9155,"g":0.0,"t":0.0845}},"tsl":[1,5,1],"uniprot":[{"acc":"Q9P212","entry":"PLCE1_HUMAN"},{"acc":"Q9P212-2","entry":"PLCE1_HUMAN"},{"acc":"Q9P212-2","entry":"PLCE1_HUMAN"}],"varity":{"er":{"rankscore":0.39571,"score":0.17285545},"er_loo":{"rankscore":0.3957,"score":0.17285545},"r":{"rankscore":0.41469,"score":0.19642633},"r_loo":{"rankscore":0.41469,"score":0.19642633}},"vep_canonical":"YES","vest4":{"rankscore":0.08366,"score":[0.101,0.086,0.085]},"vindijia_neandertal":["C","C"]},"hg38":{"end":94298382,"start":94298382},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"7991","position":"5805"},"cds":{"length":"6909","position":"5171"},"effect":"missense_variant","feature_id":"NM_016341.3","feature_type":"transcript","gene_id":"PLCE1","genename":"PLCE1","hgvs_c":"c.5171C>T","hgvs_p":"p.Ser1724Phe","protein":{"length":"2302","position":"1724"},"putative_impact":"MODERATE","rank":"24","total":"33","transcript_biotype":"protein_coding"},{"cdna":{"length":"7943","position":"5757"},"cds":{"length":"6861","position":"5123"},"effect":"missense_variant","feature_id":"NM_001288989.1","feature_type":"transcript","gene_id":"PLCE1","genename":"PLCE1","hgvs_c":"c.5123C>T","hgvs_p":"p.Ser1708Phe","protein":{"length":"2286","position":"1708"},"putative_impact":"MODERATE","rank":"24","total":"33","transcript_biotype":"protein_coding"},{"cdna":{"length":"6502","position":"4316"},"cds":{"length":"5985","position":"4247"},"effect":"missense_variant","feature_id":"NM_001165979.2","feature_type":"transcript","gene_id":"PLCE1","genename":"PLCE1","hgvs_c":"c.4247C>T","hgvs_p":"p.Ser1416Phe","protein":{"length":"1994","position":"1416"},"putative_impact":"MODERATE","rank":"23","total":"32","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"T","position":"94298382","ref":"C"}}