{"_id":"chr21:g.27264041A>C","_version":1,"cadd":{"_license":"http://bit.ly/2TIuab9","alt":"C","anc":"A","annotype":"CodingTranscript","bstatistic":825,"chmm":{"bivflnk":0.0,"enh":0.008,"enhbiv":0.0,"het":0.0,"quies":0.118,"reprpc":0.0,"reprpcwk":0.008,"tssa":0.0,"tssaflnk":0.0,"tssbiv":0.0,"tx":0.465,"txflnk":0.0,"txwk":0.386,"znfrpts":0.008},"chrom":21,"consdetail":"missense","consequence":"NON_SYNONYMOUS","consscore":7,"cpg":0.03,"dna":{"helt":-0.74,"mgw":0.56,"prot":4.36,"roll":5.99},"dst2splice":8,"dst2spltype":"DONOR","encode":{"exp":9131.42,"h3k27ac":4.04,"h3k4me1":9.0,"h3k4me3":3.0,"nucleo":1.2},"exon":"17/18","fitcons":0.701516,"gc":0.42,"gene":{"ccds_id":"CCDS13576.1","cds":{"cdna_pos":2238,"cds_pos":2204,"rel_cdna_pos":0.65,"rel_cds_pos":0.95},"feature_id":"ENST00000346798","gene_id":"ENSG00000142192","genename":"APP","prot":{"domain":"ndomain","protpos":735,"rel_prot_pos":0.95}},"gerp":{"n":5.65,"rs":659.2,"rs_pval":2.97824e-172,"s":5.65},"grantham":109,"isderived":"TRUE","isknownvariant":"FALSE","istv":"TRUE","length":0,"mapability":{"20bp":1,"35bp":1},"min_dist_tse":70,"min_dist_tss":6255,"mutindex":-28,"naa":"G","oaa":"V","phast_cons":{"mammalian":0.997,"primate":0.916,"vertebrate":1.0},"phred":27.8,"phylop":{"mammalian":2.276,"primate":0.53,"vertebrate":4.743},"polyphen":{"cat":"probably_damaging","val":0.995},"pos":27264041,"rawscore":5.987781,"ref":"A","segway":"R1","sift":{"cat":"deleterious","val":0},"type":"SNV"},"chrom":"21","dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"G","codon_degeneracy":[0,0,0,0,0,0,0,0],"codonpos":[2,2,2,2,2,2,2,2],"pos":[735,604,660,716,625,711,679,717],"ref":"V","refcodon":["GTG","GTG","GTG","GTG","GTG","GTG","GTG","GTG"]},"alphamissense":{"pred":["P","P","P","P","P","P","P","P"],"rankscore":0.87237,"score":[0.9372,0.9311,0.9126,0.9316,0.953,0.8993,0.9352,0.9278]},"alt":"C","altai_neandertal":["A","A"],"ancestral_allele":"A","appris":["principal4","alternative1","alternative1","alternative1"],"bayesdel":{"add_af":{"pred":"D","rankscore":0.94932,"score":0.521925},"no_af":{"pred":"D","rankscore":0.94858,"score":0.511932}},"bstatistic":{"converted_rankscore":0.013,"score":993.0},"chagyrskaya_neandertal":["A","A"],"chrom":"21","clinpred":{"pred":"D","rankscore":0.84541,"score":0.993659794330597},"dann":{"rankscore":0.80591,"score":0.9970060225238208},"denisova":["A","A"],"deogen2":{"pred":"D","rankscore":0.91938,"score":0.716061},"eigen":{"phred_coding":8.007291,"raw_coding":0.757595407104976,"raw_coding_rankscore":0.83401},"eigen-pc":{"phred_coding":9.198801,"raw_coding":0.76631678813955,"raw_coding_rankscore":0.87372},"ensembl":{"geneid":["ENSG00000142192","ENSG00000142192","ENSG00000142192","ENSG00000142192","ENSG00000142192","ENSG00000142192","ENSG00000142192","ENSG00000142192"],"proteinid":["ENSP00000284981","ENSP00000346129","ENSP00000345463","ENSP00000350578","ENSP00000352760","ENSP00000387483","ENSP00000398879","ENSP00000351796"],"transcriptid":["ENST00000346798","ENST00000354192","ENST00000348990","ENST00000357903","ENST00000359726","ENST00000440126","ENST00000439274","ENST00000358918"]},"esm1b":{"pred":["D","D","D","D","D","D"],"rankscore":0.91931,"score":[-12.868,-13.669,-13.572,-13.408,-13.424,-13.351]},"eve":{"class10_pred":"U","class20_pred":"U","class25_pred":"U","class30_pred":"U","class40_pred":"U","class50_pred":"U","class60_pred":"U","class70_pred":"U","class75_pred":"U","class80_pred":"U","class90_pred":"U","rankscore":0.56544,"score":0.4880338200494661},"fathmm":{"converted_rankscore":0.96243,"pred":["D","D","D","D","D","D","D"],"score":[-3.97,-3.97,-3.97,-3.97,-3.97,-3.97,-3.97]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.95738,"coding_score":0.99415},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.9621,"coding_score":0.949444},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.6231,"score":0.659464},"h1-hesc":{"confidence_value":0,"rankscore":0.87919,"score":0.724815},"huvec":{"confidence_value":0,"rankscore":0.83352,"score":0.714379},"integrated":{"confidence_value":0,"rankscore":0.73137,"score":0.706548}},"gencode_basic":["Y","Y","Y","Y","Y","Y","Y","Y"],"genename":["APP","APP","APP","APP","APP","APP","APP","APP"],"genocanyon":{"rankscore":0.74766,"score":0.99999999994553},"gerp":{"91_mammals":{"rankscore":0.77318,"score":4.05}},"gerp++":{"nr":5.65,"rs":5.65,"rs_rankscore":0.86881},"gmvp":{"rankscore":0.98841,"score":0.9884740985983483},"hg18":{"end":26185912,"start":26185912},"hg19":{"end":27264041,"start":27264041},"hg38":{"end":25891729,"start":25891729},"hgvsc":["c.1874T>G","c.1811T>G","c.2036T>G","c.2147T>G","c.2204T>G","c.1979T>G","c.2150T>G","c.2132T>G"],"hgvsp":["p.Val735Gly","p.Val625Gly","p.V717G","p.Val711Gly","p.Val679Gly","p.V716G","p.Val716Gly","p.Val604Gly","p.Val660Gly","p.V604G","p.V711G","p.V660G","p.V625G","p.Val717Gly","p.V735G","p.V679G"],"interpro":{"domain":["Beta-amyloid precursor protein C-terminal","Beta-amyloid precursor protein C-terminal","Beta-amyloid precursor protein C-terminal"]},"list-s2":{"pred":["D","D","D","D","D","D","D","D"],"rankscore":0.69449,"score":[0.914409,0.914409,0.914409,0.914409,0.914409,0.914409,0.914409,0.914409]},"lrt":{"converted_rankscore":0.62929,"omega":0.056475,"pred":"D","score":1e-6},"m-cap":{"pred":"D","rankscore":0.94667,"score":0.470222},"metalr":{"pred":"D","rankscore":0.96909,"score":0.9068},"metarnn":{"pred":["D","D","D","D","D","D","D","D"],"rankscore":0.73992,"score":[0.726238,0.726238,0.726238,0.726238,0.726238,0.726238,0.72623813,0.72623813]},"metasvm":{"pred":"D","rankscore":0.9781,"score":1.0349},"mpc":{"rankscore":0.8521,"score":1.40099854418},"mutationassessor":{"pred":"L","rankscore":0.29295,"score":1.15},"mutationtaster":{"aae":["V735G","V604G","V660G","V716G","V679G","V717G","V679G","V711G","V625G"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae"],"pred":["D","D","D","D","D","D","D","D","D"],"score":[1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0]},"mutformer":{"rankscore":0.98028,"score":0.9963076},"mutpred":{"aa_change":"V735G","accession":"P05067","pred":{"mechanism":"Loss of stability","p_val":0.0148},"rankscore":0.90388,"score":0.779},"mvp":{"rankscore":0.99579,"score":[0.995846991087,0.995846991087,0.995846991087,0.995846991087,0.995846991087,0.995846991087,0.995846991087,0.995846991087]},"phactboost":{"rankscore":0.94582,"score":0.998524313267617},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.57723,"score":0.979},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.92042,"score":8.881},"17way_primate":{"rankscore":0.94297,"score":0.756},"470way_mammalian":{"rankscore":0.86698,"score":11.127}},"polyphen2":{"hdiv":{"pred":["D","D","D","D","D"],"rankscore":0.90584,"score":[0.999,1.0,0.981,0.981,0.999]},"hvar":{"pred":["D","D","D","D","D"],"rankscore":0.8111,"score":[0.993,0.988,0.978,0.978,0.993]}},"primateai":{"pred":"T","rankscore":0.5616,"score":0.623051285744},"provean":{"converted_rankscore":0.9014,"pred":["D","D","D","D","D","D","D"],"score":[-6.04,-5.75,-5.53,-6.04,-6.04,-5.78,-6.14]},"ref":"A","reliability_index":10,"revel":{"rankscore":0.99221,"score":[0.955,0.955,0.955,0.955,0.955,0.955,0.955,0.955]},"sift":{"converted_rankscore":0.91255,"pred":["D","D","D","D","D","D","D"],"score":[0.001,0.0,0.0,0.001,0.001,0.001,0.001]},"sift4g":{"converted_rankscore":0.92824,"pred":["D","D","D","D","D","D","D","D"],"score":[0.0,0.001,0.001,0.0,0.001,0.001,0.001,0.0]},"siphy_29way":{"logodds_rankscore":0.78608,"logodds_score":15.8391,"pi":{"a":1.0,"c":0.0,"g":0.0,"t":0.0}},"tsl":[1,1,1,1,2,2,1,5],"uniprot":[{"acc":"P05067","entry":"A4_HUMAN"},{"acc":"P05067-10","entry":"A4_HUMAN"},{"acc":"P05067-4","entry":"A4_HUMAN"},{"acc":"P05067-8","entry":"A4_HUMAN"},{"acc":"A0A0A0MRG2","entry":"A0A0A0MRG2_HUMAN"},{"acc":"P05067-11","entry":"A4_HUMAN"},{"acc":"E9PG40","entry":"E9PG40_HUMAN"},{"acc":"P05067-9","entry":"A4_HUMAN"}],"varity":{"er":{"rankscore":0.93927,"score":0.8851975},"er_loo":{"rankscore":0.93927,"score":0.8851975},"r":{"rankscore":0.89241,"score":0.874763},"r_loo":{"rankscore":0.89243,"score":0.874763}},"vep_canonical":"YES","vest4":{"rankscore":0.66443,"score":[0.591,0.512,0.494,0.504,0.511,0.611,0.654,0.591]},"vindijia_neandertal":["A","A"]},"hg19":{"end":27264041,"start":27264041},"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"3633","position":"2404"},"cds":{"length":"2313","position":"2204"},"effect":"missense_variant","feature_id":"NM_000484.3","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2204T>G","hgvs_p":"p.Val735Gly","protein":{"length":"770","position":"735"},"putative_impact":"MODERATE","rank":"17","total":"18","transcript_biotype":"protein_coding"},{"cdna":{"length":"3557","position":"2328"},"cds":{"length":"2241","position":"2132"},"effect":"missense_variant","feature_id":"NM_001136016.3","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2132T>G","hgvs_p":"p.Val711Gly","protein":{"length":"746","position":"711"},"putative_impact":"MODERATE","rank":"16","total":"17","transcript_biotype":"protein_coding"},{"cdna":{"length":"3240","position":"2011"},"cds":{"length":"1920","position":"1811"},"effect":"missense_variant","feature_id":"NM_001136129.2","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.1811T>G","hgvs_p":"p.Val604Gly","protein":{"length":"639","position":"604"},"putative_impact":"MODERATE","rank":"14","total":"15","transcript_biotype":"protein_coding"},{"cdna":{"length":"3465","position":"2236"},"cds":{"length":"2145","position":"2036"},"effect":"missense_variant","feature_id":"NM_001136130.2","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2036T>G","hgvs_p":"p.Val679Gly","protein":{"length":"714","position":"679"},"putative_impact":"MODERATE","rank":"16","total":"17","transcript_biotype":"protein_coding"},{"cdna":{"length":"3579","position":"2350"},"cds":{"length":"2259","position":"2150"},"effect":"missense_variant","feature_id":"NM_001204301.1","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2150T>G","hgvs_p":"p.Val717Gly","protein":{"length":"752","position":"717"},"putative_impact":"MODERATE","rank":"16","total":"17","transcript_biotype":"protein_coding"},{"cdna":{"length":"3522","position":"2293"},"cds":{"length":"2202","position":"2093"},"effect":"missense_variant","feature_id":"NM_001204302.1","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2093T>G","hgvs_p":"p.Val698Gly","protein":{"length":"733","position":"698"},"putative_impact":"MODERATE","rank":"15","total":"16","transcript_biotype":"protein_coding"},{"cdna":{"length":"3354","position":"2125"},"cds":{"length":"2034","position":"1925"},"effect":"missense_variant","feature_id":"NM_001204303.1","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.1925T>G","hgvs_p":"p.Val642Gly","protein":{"length":"677","position":"642"},"putative_impact":"MODERATE","rank":"14","total":"15","transcript_biotype":"protein_coding"},{"cdna":{"length":"3576","position":"2347"},"cds":{"length":"2256","position":"2147"},"effect":"missense_variant","feature_id":"NM_201413.2","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.2147T>G","hgvs_p":"p.Val716Gly","protein":{"length":"751","position":"716"},"putative_impact":"MODERATE","rank":"16","total":"17","transcript_biotype":"protein_coding"},{"cdna":{"length":"3408","position":"2179"},"cds":{"length":"2088","position":"1979"},"effect":"missense_variant","feature_id":"NM_201414.2","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.1979T>G","hgvs_p":"p.Val660Gly","protein":{"length":"695","position":"660"},"putative_impact":"MODERATE","rank":"15","total":"16","transcript_biotype":"protein_coding"},{"cdna":{"length":"3295","position":"2066"},"cds":{"length":"1983","position":"1874"},"effect":"missense_variant","feature_id":"NM_001136131.2","feature_type":"transcript","gene_id":"APP","genename":"APP","hgvs_c":"c.1874T>G","hgvs_p":"p.Val625Gly","protein":{"length":"660","position":"625"},"putative_impact":"MODERATE","rank":"15","total":"16","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"C","position":"27264041","ref":"A"}}