{"_id":"chr14:g.73170839C>T","_version":1,"chrom":"14","clingen":{"caid":"CA390302559"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"F","codon_degeneracy":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"codonpos":[1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1],"pos":[40,40,40,40,44,40,40,44,40,44,40,44,44,40,40,40,44],"ref":"L","refcodon":["CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT","CTT"]},"alphamissense":{"pred":["B","B","B","B","B","B","B","B","B","B","B","B","B","B","B"],"rankscore":0.06571,"score":[0.0609,0.0774,0.0638,0.0641,0.0621,0.0639,0.0654,0.0684,0.0626,0.0606,0.0624,0.0774,0.0611,0.0772,0.0591]},"alt":"T","altai_neandertal":["C","C"],"ancestral_allele":"C","appris":["alternative1","principal4","alternative1"],"bayesdel":{"add_af":{"pred":"D","rankscore":0.67429,"score":0.130712},"no_af":{"pred":"D","rankscore":0.67022,"score":-0.050018}},"bstatistic":{"converted_rankscore":0.4951,"score":768.0},"cadd":{"phred":10.75,"raw_rankscore":0.14168,"raw_score":1.036652},"cds_strand":["+","+","+","+","+","+","+","+","+","+","+","+","+","+","+","+","+"],"chagyrskaya_neandertal":["C","C"],"chrom":"14","clinpred":{"pred":"T","rankscore":0.00409,"score":0.0164244491606951},"dann":{"rankscore":0.10172,"score":0.7300358106803565},"denisova":["C","C"],"deogen2":{"pred":["T","T","T","T"],"rankscore":0.74555,"score":[0.015575,0.029244,0.383771,0.009564]},"eigen":{"phred_coding":0.3288537,"raw_coding":-1.07531456635194,"raw_coding_rankscore":0.07101},"eigen-pc":{"phred_coding":0.4153549,"raw_coding":-1.06257323371626,"raw_coding_rankscore":0.08446},"ensembl":{"geneid":["ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815","ENSG00000080815"],"proteinid":["ENSP00000451498","ENSP00000451588","ENSP00000452128","ENSP00000450551","ENSP00000451880","ENSP00000451674","ENSP00000452477","ENSP00000377712","ENSP00000350342","ENSP00000326366","ENSP00000453466","ENSP00000450652","ENSP00000451915","ENSP00000451347","ENSP00000377719","ENSP00000452267","ENSP00000451429"],"transcriptid":["ENST00000557356","ENST00000556864","ENST00000556533","ENST00000556951","ENST00000557293","ENST00000553719","ENST00000553599","ENST00000394157","ENST00000357710","ENST00000324501","ENST00000560005","ENST00000555254","ENST00000554131","ENST00000557037","ENST00000394164","ENST00000556066","ENST00000557511"]},"esm1b":{"pred":["T","T","T","T","T"],"rankscore":0.36469,"score":[-4.912,-4.893,-4.918,-4.893,-4.966]},"fathmm":{"converted_rankscore":0.99592,"pred":["D","D","D","D","D","D","D","D","D","D","D","D","D","D"],"score":[-5.41,-3.23,-3.06,-3.38,-5.75,-3.23,-6.26,-6.09,-6.09,-3.99,-5.83,-3.79,-6.09,-6.06]},"fathmm-mkl":{"coding_group":"AEFDGBHI","coding_pred":"N","coding_rankscore":0.2567,"coding_score":0.37037},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.34381,"coding_score":0.218855},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.89359,"score":0.724815},"h1-hesc":{"confidence_value":0,"rankscore":0.63334,"score":0.696144},"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"],"genename":["PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1","PSEN1"],"genocanyon":{"rankscore":0.39898,"score":0.999472535452546},"gerp":{"91_mammals":{"rankscore":0.40407,"score":2.07}},"gerp++":{"nr":5.01,"rs":0.979,"rs_rankscore":0.18864},"gmvp":{"rankscore":0.16619,"score":0.16699757544413033},"hg18":{"end":72707300,"start":72707300},"hg19":{"end":73637547,"start":73637547},"hg38":{"end":73170839,"start":73170839},"hgvsc":["c.118C>T","c.130C>T"],"hgvsp":["p.L40F","p.Leu44Phe","p.Leu40Phe","p.L44F"],"list-s2":{"pred":["T","T","T","T","T","T","T","T","T","T","T","T","T","T","T"],"rankscore":0.41649,"score":[0.757724,0.781422,0.752925,0.752925,0.762324,0.752925,0.734227,0.756924,0.752925,0.757724,0.752925,0.781422,0.755524,0.772923,0.738226]},"lrt":{"converted_rankscore":0.11851,"omega":0.740232,"pred":"N","score":0.510318},"m-cap":{"pred":"D","rankscore":0.90725,"score":0.296024},"metalr":{"pred":"D","rankscore":0.96809,"score":0.9038},"metarnn":{"pred":["T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T"],"rankscore":0.2032,"score":[0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544,0.109021544]},"metasvm":{"pred":"D","rankscore":0.94747,"score":0.8272},"mpc":{"rankscore":0.54033,"score":0.583003539302},"mutationassessor":{"pred":["N","N","N"],"rankscore":0.16971,"score":[0.69,0.69,0.69]},"mutationtaster":{"aae":["L44F","L40F","L44F","L40F","L44F","L44F","L44F"],"converted_rankscore":0.18612,"model":["simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","simple_aae","without_aae"],"pred":["N","N","N","N","N","N","N","N"],"score":[1.0,1.0,1.0,1.0,1.0,1.0,1.0,0.99998]},"mutformer":{"rankscore":0.98072,"score":0.9964579},"mutpred":{"aa_change":["L44F","L44F","L44F","L44F","L44F","L44F"],"accession":["P49768","P49768","P49768","P49768","P49768","P49768"],"pred":[{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214},{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214},{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214},{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214},{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214},{"mechanism":"Gain of catalytic residue at H46","p_val":0.0214}],"rankscore":0.10571,"score":[0.194,0.194,0.194,0.194,0.194,0.194]},"mvp":{"rankscore":0.84332,"score":[0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406,0.844809897406]},"phactboost":{"rankscore":0.27994,"score":0.0167720553231687},"phastcons":{"100way_vertebrate":{"rankscore":0.17386,"score":0.006},"17way_primate":{"rankscore":0.18284,"score":0.1},"470way_mammalian":{"rankscore":0.28453,"score":0.927}},"phylop":{"100way_vertebrate":{"rankscore":0.35516,"score":1.521},"17way_primate":{"rankscore":0.09635,"score":-0.187},"470way_mammalian":{"rankscore":0.32053,"score":2.307}},"polyphen2":{"hdiv":{"pred":["B","B","B","B"],"rankscore":0.32818,"score":[0.311,0.0,0.016,0.0]},"hvar":{"pred":["B","B","B","B"],"rankscore":0.30765,"score":[0.101,0.004,0.007,0.004]}},"primateai":{"pred":"T","rankscore":0.01448,"score":0.222322434187},"provean":{"converted_rankscore":0.45042,"pred":["N","N","N","N","N","N","N","N","N","N","N","N","N","N","N","N","N"],"score":[-0.62,-1.94,-0.85,-0.85,-0.51,-0.68,-0.85,-0.39,-0.45,-0.53,-0.78,-0.36,-0.46,-1.94,-0.45,-1.94,-0.17]},"ref":"C","reliability_index":10,"revel":{"rankscore":0.75889,"score":[0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462,0.462]},"sift":{"converted_rankscore":0.16358,"pred":["T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T"],"score":[0.404,0.705,0.71,0.71,0.633,0.702,0.71,0.703,0.264,0.653,0.703,0.702,0.709,0.705,0.264,0.705,0.408]},"sift4g":{"converted_rankscore":0.45961,"pred":["T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T","T"],"score":[0.06,0.713,0.06,0.06,0.075,0.059,0.06,0.092,0.103,0.172,0.061,0.067,0.074,0.713,0.103,0.43,0.193]},"siphy_29way":{"logodds_rankscore":0.43222,"logodds_score":10.3687,"pi":{"a":0.1823,"c":0.3086,"g":0.5091,"t":0.0}},"tsl":[4,5,5,2,2,2,4,2,1,1,3,3,3,4,1,3,5],"uniprot":[{"acc":"G3V3Z0","entry":"G3V3Z0_HUMAN"},{"acc":"G3V449","entry":"G3V449_HUMAN"},{"acc":"G3V519","entry":"G3V519_HUMAN"},{"acc":"G3V2B1","entry":"G3V2B1_HUMAN"},{"acc":"G3V4M0","entry":"G3V4M0_HUMAN"},{"acc":"G3V499","entry":"G3V499_HUMAN"},{"acc":"G3V2B1","entry":"G3V2B1_HUMAN"},{"acc":"P49768-4","entry":"PSN1_HUMAN"},{"acc":"P49768-2","entry":"PSN1_HUMAN"},{"acc":"P49768","entry":"PSN1_HUMAN"},{"acc":"H0YM52","entry":"H0YM52_HUMAN"},{"acc":"G3V2G7","entry":"G3V2G7_HUMAN"},{"acc":"G3V4P4","entry":"G3V4P4_HUMAN"},{"acc":"G3V3P0","entry":"G3V3P0_HUMAN"},{"acc":"P49768-2","entry":"PSN1_HUMAN"},{"acc":"G3V5B1","entry":"G3V5B1_HUMAN"},{"acc":"P49768-6","entry":"PSN1_HUMAN"}],"varity":{"er":{"rankscore":0.03472,"score":0.037674412},"er_loo":{"rankscore":0.03471,"score":0.037674412},"r":{"rankscore":0.00586,"score":0.020321205},"r_loo":{"rankscore":0.00586,"score":0.020321205}},"vep_canonical":"YES","vest4":{"rankscore":0.29544,"score":[0.212,0.234,0.239,0.234,0.261]},"vindijia_neandertal":["C","C"]},"hg38":{"end":73170839,"start":73170839},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"6090","position":"414"},"cds":{"length":"1404","position":"130"},"effect":"missense_variant","feature_id":"NM_000021.3","feature_type":"transcript","gene_id":"PSEN1","genename":"PSEN1","hgvs_c":"c.130C>T","hgvs_p":"p.Leu44Phe","protein":{"length":"467","position":"44"},"putative_impact":"MODERATE","rank":"4","total":"12","transcript_biotype":"protein_coding"},{"cdna":{"length":"6078","position":"402"},"cds":{"length":"1392","position":"118"},"effect":"missense_variant","feature_id":"NM_007318.2","feature_type":"transcript","gene_id":"PSEN1","genename":"PSEN1","hgvs_c":"c.118C>T","hgvs_p":"p.Leu40Phe","protein":{"length":"463","position":"40"},"putative_impact":"MODERATE","rank":"4","total":"12","transcript_biotype":"protein_coding"}]},"vcf":{"alt":"T","position":"73170839","ref":"C"}}