{"_id":"chr21:g.36767244A>C","_version":1,"chrom":"21","clingen":{"caid":"CA409921845"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"S","codon_degeneracy":[0,0,0],"codonpos":[2,2,2],"pos":[498,498,498],"ref":"I","refcodon":["ATC","ATC","ATC"]},"alphamissense":{"pred":["P","P"],"rankscore":0.74312,"score":[0.7315,0.7325]},"alt":"C","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":["principal1","principal1","principal1"],"bayesdel":{"add_af":{"pred":"D","rankscore":0.94181,"score":0.496365},"no_af":{"pred":"D","rankscore":0.94104,"score":0.475218}},"bstatistic":{"converted_rankscore":0.11584,"score":947.0},"cadd":{"phred":22.6,"raw_rankscore":0.48188,"raw_score":3.458218},"chagyrskaya_neandertal":["A","A"],"chrom":"21","clinpred":{"pred":"D","rankscore":0.74634,"score":0.982672810554504},"dann":{"rankscore":0.73572,"score":0.99590091185744},"denisova":["A","A"],"deogen2":{"pred":["D","D","D"],"rankscore":0.96288,"score":[0.840884,0.840884,0.840884]},"eigen":{"phred_coding":7.461764,"raw_coding":0.723579918302779,"raw_coding_rankscore":0.81179},"eigen-pc":{"phred_coding":7.98015,"raw_coding":0.711850913043513,"raw_coding_rankscore":0.83277},"ensembl":{"geneid":["ENSG00000159267","ENSG00000159267","ENSG00000159267"],"proteinid":["ENSP00000479939","ENSP00000338387","ENSP00000382071"],"transcriptid":["ENST00000612277","ENST00000336648","ENST00000399120"]},"esm1b":{"pred":["D","D","D"],"rankscore":0.76939,"score":[-10.516,-10.516,-10.516]},"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":0.92796,"score":[0.8658023338601013,0.8658023338601013,0.8658023338601013]},"fathmm":{"converted_rankscore":0.94693,"pred":["D","D"],"score":[-3.51,-3.51]},"fathmm-mkl":{"coding_group":"AEFDI","coding_pred":"D","coding_rankscore":0.9029,"coding_score":0.99036},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.8139,"coding_score":0.884318},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.63936,"score":0.670034},"h1-hesc":{"confidence_value":0,"rankscore":0.79029,"score":0.719019},"huvec":{"confidence_value":0,"rankscore":0.61905,"score":0.655142},"integrated":{"confidence_value":0,"rankscore":0.43195,"score":0.638212}},"gencode_basic":["Y","Y","Y"],"genename":["HLCS","HLCS","HLCS"],"genocanyon":{"rankscore":0.74766,"score":0.999999973439395},"gerp":{"91_mammals":{"rankscore":0.98311,"score":6.17}},"gerp++":{"nr":6.11,"rs":6.11,"rs_rankscore":0.99132},"gmvp":{"rankscore":0.94739,"score":0.9475632333540625},"hg18":{"end":37061415,"start":37061415},"hg19":{"end":38139545,"start":38139545},"hg38":{"end":36767244,"start":36767244},"hgvsc":"c.1493T>G","hgvsp":["p.Ile498Ser","p.I498S"],"interpro":{"domain":["Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain|Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain","Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain|Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain","Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain|Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain"]},"list-s2":{"pred":"D","rankscore":0.65253,"score":0.90001},"lrt":{"converted_rankscore":0.8433,"omega":0.051298,"pred":"D","score":1e-6},"m-cap":{"pred":"D","rankscore":0.91738,"score":0.330566},"metalr":{"pred":"D","rankscore":0.96095,"score":0.8824},"metarnn":{"pred":["D","D","D"],"rankscore":0.93189,"score":[0.93861365,0.93861365,0.93861365]},"metasvm":{"pred":"D","rankscore":0.96273,"score":0.9418},"mpc":{"rankscore":0.60098,"score":0.68226045739},"mutationassessor":{"pred":["M","M","M"],"rankscore":0.56016,"score":[2.045,2.045,2.045]},"mutationtaster":{"aae":["I498S","I498S"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae"],"pred":["D","D"],"score":[1.0,1.0]},"mutformer":{"rankscore":0.93119,"score":0.9446471},"mutpred":{"aa_change":["I498S","I498S","I498S"],"accession":["P50747","P50747","P50747"],"pred":[{"mechanism":"Gain of disorder","p_val":0.0234},{"mechanism":"Gain of disorder","p_val":0.0234},{"mechanism":"Gain of disorder","p_val":0.0234}],"rankscore":0.812,"score":[0.674,0.674,0.674]},"mvp":{"rankscore":0.9908,"score":[0.990904939986,0.990904939986,0.990904939986]},"phactboost":{"rankscore":0.79745,"score":[0.943994642123564,0.943994642123564,0.943994642123564]},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.22948,"score":0.238},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.89323,"score":8.081},"17way_primate":{"rankscore":0.94297,"score":0.756},"470way_mammalian":{"rankscore":0.87239,"score":11.147}},"polyphen2":{"hdiv":{"pred":["D","D","D"],"rankscore":0.55135,"score":[0.959,0.959,0.959]},"hvar":{"pred":["P","P","P"],"rankscore":0.58608,"score":[0.81,0.81,0.81]}},"primateai":{"pred":"T","rankscore":0.38396,"score":0.496905356646},"provean":{"converted_rankscore":0.77965,"pred":["D","D"],"score":[-4.48,-4.48]},"ref":"A","reliability_index":10,"revel":{"rankscore":0.97624,"score":[0.911,0.911]},"sift":{"converted_rankscore":0.7849,"pred":["D","D"],"score":[0.001,0.001]},"sift4g":{"converted_rankscore":0.83351,"pred":["D","D","D"],"score":[0.001,0.001,0.001]},"siphy_29way":{"logodds_rankscore":0.85216,"logodds_score":16.7021,"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":0.82606,"score":[0.70492995,0.70492995,0.70492995]},"er_loo":{"rankscore":0.82607,"score":[0.70492995,0.70492995,0.70492995]},"r":{"rankscore":0.84553,"score":[0.809988,0.809988,0.809988]},"r_loo":{"rankscore":0.84554,"score":[0.809988,0.809988,0.809988]}},"vep_canonical":"YES","vest4":{"rankscore":0.92433,"score":[0.921,0.921,0.92]},"vindijia_neandertal":["A","A"]},"hg38":{"end":36767244,"start":36767244},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"6019","position":"1973"},"cds":{"length":"2181","position":"1493"},"effect":"missense_variant","feature_id":"NM_000411.6","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1493T>G","hgvs_p":"p.Ile498Ser","protein":{"length":"726","position":"498"},"putative_impact":"MODERATE","rank":"8","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6953","position":"2907"},"cds":{"length":"2181","position":"1493"},"effect":"missense_variant","feature_id":"NM_001242784.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1493T>G","hgvs_p":"p.Ile498Ser","protein":{"length":"726","position":"498"},"putative_impact":"MODERATE","rank":"8","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6112","position":"2066"},"cds":{"length":"2181","position":"1493"},"effect":"missense_variant","feature_id":"NM_001242785.1","feature_type":"transcript","gene_id":"HLCS","genename":"HLCS","hgvs_c":"c.1493T>G","hgvs_p":"p.Ile498Ser","protein":{"length":"726","position":"498"},"putative_impact":"MODERATE","rank":"8","total":"12","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"C","position":"36767244","ref":"A"}}