{"_id":"chr21:g.38302564A>T","_version":1,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"T","anc":"A","annotype":"CodingTranscript","bstatistic":855,"chmm":{"bivflnk":0.0,"enh":0.024,"enhbiv":0.0,"het":0.0,"quies":0.134,"reprpc":0.0,"reprpcwk":0.0,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.087,"txflnk":0.0,"txwk":0.709,"znfrpts":0.0},"chrom":21,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.07,"dna":{"helt":-1.91,"mgw":1.34,"prot":3.74,"roll":10.63},"dst2splice":14,"dst2spltype":"DONOR","encode":{"exp":33.53,"h3k27ac":3.0,"h3k4me1":12.48,"h3k4me3":3.56,"nucleo":2.7},"exon":"6/12","fitcons":0.625622,"gc":0.56,"gene":{"ccds_id":"CCDS13647.1","cds":{"cdna_pos":2397,"cds_pos":1166,"rel_cdna_pos":0.37,"rel_cds_pos":0.53},"feature_id":"ENST00000399120","gene_id":"ENSG00000159267","genename":"HLCS","prot":{"protpos":389,"rel_prot_pos":0.54}},"gerp":{"n":5.14,"s":5.14},"grantham":113,"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":33694,"min_dist_tss":154,"mutindex":-4,"naa":"Q","oaa":"L","phast_cons":{"mammalian":0.057,"primate":0.106,"vertebrate":0.929},"phred":22.5,"phylop":{"mammalian":2.058,"primate":0.525,"vertebrate":4.188},"pos":38302564,"rawscore":3.11227,"ref":"A","segway":"R5","sift":{"cat":"deleterious","val":0},"type":"SNV"},"chrom":"21","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"Q","codon_degeneracy":[0,0,0],"codonpos":[2,2,2],"pos":[389,389,389],"ref":"L","refcodon":["CTG","CTG","CTG"]},"alphamissense":{"pred":["P","A"],"rankscore":0.68243,"score":[0.5846,0.5538]},"alt":"T","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":["principal1","principal1","principal1"],"bayesdel":{"add_af":{"pred":"D","rankscore":0.94649,"score":0.51248},"no_af":{"pred":"D","rankscore":0.94571,"score":0.498365}},"bstatistic":{"converted_rankscore":0.20147,"score":917.0},"chagyrskaya_neandertal":["A","A"],"chrom":"21","clinpred":{"pred":"D","rankscore":0.83939,"score":0.993227064609528},"dann":{"rankscore":0.5612,"score":0.9922825066090482},"denisova":["A","A"],"deogen2":{"pred":["D","D","D"],"rankscore":0.9836,"score":[0.912349,0.912349,0.912349]},"eigen":{"phred_coding":4.936244,"raw_coding":0.487002668882667,"raw_coding_rankscore":0.6633},"eigen-pc":{"phred_coding":4.056223,"raw_coding":0.35535571120476,"raw_coding_rankscore":0.58832},"ensembl":{"geneid":["ENSG00000159267","ENSG00000159267","ENSG00000159267"],"proteinid":["ENSP00000479939","ENSP00000338387","ENSP00000382071"],"transcriptid":["ENST00000612277","ENST00000336648","ENST00000399120"]},"esm1b":{"pred":["D","D","D"],"rankscore":0.87232,"score":[-12.507,-12.507,-12.507]},"eve":{"class10_pred":["U","U","U"],"class20_pred":["U","U","U"],"class25_pred":["P","P","P"],"class30_pred":["P","P","P"],"class40_pred":["P","P","P"],"class50_pred":["P","P","P"],"class60_pred":["P","P","P"],"class70_pred":["P","P","P"],"class75_pred":["P","P","P"],"class80_pred":["P","P","P"],"class90_pred":["P","P","P"],"rankscore":0.92754,"score":[0.8651987504377998,0.8651987504377998,0.8651987504377998]},"fathmm":{"converted_rankscore":0.98684,"pred":["D","D"],"score":[-5.09,-5.09]},"fathmm-mkl":{"coding_group":"AEFDBCI","coding_pred":"D","coding_rankscore":0.64829,"coding_score":0.95465},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.70203,"coding_score":0.765597},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.55848,"score":0.633656},"h1-hesc":{"confidence_value":0,"rankscore":0.55881,"score":0.658983},"huvec":{"confidence_value":0,"rankscore":0.61905,"score":0.655142},"integrated":{"confidence_value":0,"rankscore":0.37627,"score":0.615465}},"gencode_basic":["Y","Y","Y"],"genename":["HLCS","HLCS","HLCS"],"genocanyon":{"rankscore":0.74766,"score":0.999999996770584},"gerp":{"91_mammals":{"rankscore":0.77088,"score":4.04}},"gerp++":{"nr":5.14,"rs":5.14,"rs_rankscore":0.70008},"gmvp":{"rankscore":0.85485,"score":0.8552266845851695},"hg18":{"end":37224434,"start":37224434},"hg19":{"end":38302564,"start":38302564},"hg38":{"end":36930264,"start":36930264},"hgvsc":"c.1166T>A","hgvsp":["p.L389Q","p.Leu389Gln"],"interpro":{"domain":["Biotin-protein ligase, N-terminal","Biotin-protein ligase, N-terminal","Biotin-protein ligase, N-terminal"]},"list-s2":{"pred":"D","rankscore":0.58316,"score":0.873813},"lrt":{"converted_rankscore":0.62929,"omega":0.067765,"pred":"D","score":0.00001},"m-cap":{"pred":"D","rankscore":0.91718,"score":0.329819},"metalr":{"pred":"D","rankscore":0.98763,"score":0.9615},"metarnn":{"pred":["D","D","D"],"rankscore":0.91922,"score":[0.92573786,0.92573786,0.92573786]},"metasvm":{"pred":"D","rankscore":0.99818,"score":1.1053},"mpc":{"rankscore":0.47955,"score":0.493579351156},"mutationassessor":{"pred":["M","M","M"],"rankscore":0.7408,"score":[2.54,2.54,2.54]},"mutationtaster":{"aae":["L389Q","L389Q"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae"],"pred":["D","D"],"score":[1.0,1.0]},"mutformer":{"rankscore":0.96159,"score":0.9856836},"mutpred":{"aa_change":["L389Q","L389Q","L389Q"],"accession":["P50747","P50747","P50747"],"pred":[{"mechanism":"Gain of disorder","p_val":0.07},{"mechanism":"Gain of disorder","p_val":0.07},{"mechanism":"Gain of disorder","p_val":0.07}],"rankscore":0.7681,"score":[0.632,0.632,0.632]},"mvp":{"rankscore":0.99869,"score":[0.998703435406,0.998703435406,0.998703435406]},"phactboost":{"rankscore":0.77593,"score":[0.920965796616681,0.920965796616681,0.920965796616681]},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.28163,"score":0.462},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.89436,"score":8.117},"17way_primate":{"rankscore":0.94297,"score":0.756},"470way_mammalian":{"rankscore":0.8465,"score":10.987}},"polyphen2":{"hdiv":{"pred":["D","D","D"],"rankscore":0.90584,"score":[1.0,1.0,1.0]},"hvar":{"pred":["D","D","D"],"rankscore":0.72692,"score":[0.972,0.972,0.972]}},"primateai":{"pred":"T","rankscore":0.29298,"score":0.430661350489},"provean":{"converted_rankscore":0.72471,"pred":["D","D"],"score":[-3.86,-3.86]},"ref":"A","reliability_index":10,"revel":{"rankscore":0.95802,"score":[0.862,0.862]},"sift":{"converted_rankscore":0.7849,"pred":["D","D"],"score":[0.001,0.001]},"sift4g":{"converted_rankscore":0.79402,"pred":["D","D","D"],"score":[0.002,0.002,0.002]},"siphy_29way":{"logodds_rankscore":0.70643,"logodds_score":14.9413,"pi":{"a":1.0,"c":0.0,"g":0.0,"t":0.0}},"tsl":[5,1,1],"uniprot":[{"acc":"P50747","entry":"BPL1_HUMAN"},{"acc":"P50747","entry":"BPL1_HUMAN"},{"acc":"P50747","entry":"BPL1_HUMAN"}],"varity":{"er":{"rankscore":0.84572,"score":[0.73898834,0.73898834,0.73898834]},"er_loo":{"rankscore":0.84573,"score":[0.73898834,0.73898834,0.73898834]},"r":{"rankscore":0.81333,"score":[0.75796366,0.75796366,0.75796366]},"r_loo":{"rankscore":0.81335,"score":[0.75796366,0.75796366,0.75796366]}},"vep_canonical":"YES","vest4":{"rankscore":0.92784,"score":[0.924,0.924,0.924]},"vindijia_neandertal":["A","A"]},"hg19":{"end":38302564,"start":38302564},"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"6019","position":"1646"},"cds":{"length":"2181","position":"1166"},"effect":"missense_variant","feature_id":"NM_000411.6","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1166T>A","hgvs_p":"p.Leu389Gln","protein":{"length":"726","position":"389"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6953","position":"2580"},"cds":{"length":"2181","position":"1166"},"effect":"missense_variant","feature_id":"NM_001242784.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1166T>A","hgvs_p":"p.Leu389Gln","protein":{"length":"726","position":"389"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6112","position":"1739"},"cds":{"length":"2181","position":"1166"},"effect":"missense_variant","feature_id":"NM_001242785.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1166T>A","hgvs_p":"p.Leu389Gln","protein":{"length":"726","position":"389"},"putative_impact":"MODERATE","rank":"6","total":"12","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"T","position":"38302564","ref":"A"}}