{"_id":"chr10:g.68199393T>C","_version":1,"chrom":"10","clingen":{"caid":"CA376858944"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"P","codon_degeneracy":[0,0,0,0],"codonpos":[2,2,2,2],"pos":[1104,829,1104,810],"ref":"L","refcodon":["CTG","CTG","CTG","CTG"]},"alphamissense":{"pred":["P","P","P","P"],"rankscore":0.89587,"score":[0.9705,0.9306,0.9711,0.9384]},"alt":"C","altai_neandertal":["T","T"],"ancestral_allele":"T","appris":["principal1","principal1"],"bayesdel":{"add_af":{"pred":"D","rankscore":0.87714,"score":0.366173},"no_af":{"pred":"D","rankscore":0.87556,"score":0.288206}},"bstatistic":{"converted_rankscore":0.16858,"score":929.0},"cadd":{"phred":26.4,"raw_rankscore":0.75923,"raw_score":4.720353},"cds_strand":["+","+","+","+"],"chagyrskaya_neandertal":["T","T"],"chrom":"10","clinpred":{"pred":"D","rankscore":0.95098,"score":0.998761177062988},"dann":{"rankscore":0.98787,"score":0.9992192684798787},"denisova":["T","T"],"deogen2":{"pred":"T","rankscore":0.46992,"score":0.137148},"eigen":{"phred_coding":8.684298,"raw_coding":0.795066953720528,"raw_coding_rankscore":0.85796},"eigen-pc":{"phred_coding":9.127833,"raw_coding":0.763492061439682,"raw_coding_rankscore":0.87164},"ensembl":{"geneid":["ENSG00000138347","ENSG00000138347","ENSG00000138347","ENSG00000138347"],"proteinid":["ENSP00000441668","ENSP00000346369","ENSP00000351790","ENSP00000480757"],"transcriptid":["ENST00000540630","ENST00000354393","ENST00000358913","ENST00000613327"]},"esm1b":{"pred":["D","D","D"],"rankscore":0.94059,"score":[-14.323,-14.245,-14.323]},"fathmm":{"converted_rankscore":0.68616,"pred":["T","T","T"],"score":[-0.35,-0.35,-0.35]},"fathmm-mkl":{"coding_group":"AEFBI","coding_pred":"D","coding_rankscore":0.81177,"coding_score":0.98276},"fathmm-xf":{"coding_pred":"D","coding_rankscore":0.99775,"coding_score":0.978633},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.36545,"score":0.588015},"h1-hesc":{"confidence_value":0,"rankscore":0.23631,"score":0.573888},"huvec":{"confidence_value":0,"rankscore":0.36253,"score":0.586402},"integrated":{"confidence_value":0,"rankscore":0.25195,"score":0.553676}},"gencode_basic":["Y","Y","Y","Y"],"genename":["MYPN","MYPN","MYPN","MYPN"],"genocanyon":{"rankscore":0.74766,"score":0.999999780783508},"gerp":{"91_mammals":{"rankscore":0.90843,"score":5.09}},"gerp++":{"nr":5.38,"rs":5.38,"rs_rankscore":0.77279},"gmvp":{"rankscore":0.9182,"score":0.9184463502393254},"hg18":{"end":69629156,"start":69629156},"hg19":{"end":69959150,"start":69959150},"hg38":{"end":68199393,"start":68199393},"hgvsc":["c.2429T>C","c.2486T>C","c.3311T>C"],"hgvsp":["p.L829P","p.Leu810Pro","p.Leu829Pro","p.L1104P","p.L810P","p.Leu1104Pro"],"interpro":{"domain":["Immunoglobulin I-set|Immunoglobulin-like domain|Immunoglobulin subtype 2|Immunoglobulin subtype","Immunoglobulin I-set|Immunoglobulin-like domain|Immunoglobulin subtype 2|Immunoglobulin subtype","Immunoglobulin I-set|Immunoglobulin-like domain|Immunoglobulin subtype 2|Immunoglobulin subtype"]},"list-s2":{"pred":["D","D","D"],"rankscore":0.76795,"score":[0.938306,0.938306,0.938306]},"lrt":{"converted_rankscore":0.62929,"omega":0.0,"pred":"D","score":6e-6},"m-cap":{"pred":"D","rankscore":0.86448,"score":0.195896},"metalr":{"pred":"D","rankscore":0.8157,"score":0.5097},"metarnn":{"pred":["D","D","D","D"],"rankscore":0.89029,"score":[0.89673984,0.89673984,0.89673984,0.89673984]},"metasvm":{"pred":"D","rankscore":0.8336,"score":0.0562},"mpc":{"rankscore":0.65421,"score":0.784066996739},"mutationassessor":{"pred":["M","M"],"rankscore":0.79844,"score":[2.73,2.73]},"mutationtaster":{"aae":["L829P","L1104P","L1104P"],"converted_rankscore":0.81001,"model":["simple_aae","simple_aae","simple_aae"],"pred":["D","D","D"],"score":[1.0,1.0,1.0]},"mutformer":{"rankscore":0.98369,"score":0.9973907},"mutpred":{"aa_change":["L1104P","L1104P"],"accession":["F5GWA6","F5GWA6"],"pred":[{"mechanism":"Gain of glycosylation at L1104","p_val":0.0087},{"mechanism":"Gain of glycosylation at L1104","p_val":0.0087}],"rankscore":0.82367,"score":[0.686,0.686]},"mvp":{"rankscore":0.92186,"score":[0.922650643041,0.922650643041,0.922650643041,0.922650643041]},"phactboost":{"rankscore":0.91172,"score":[0.995245822270259,0.995245822270259]},"phastcons":{"100way_vertebrate":{"rankscore":0.71638,"score":1.0},"17way_primate":{"rankscore":0.49496,"score":0.949},"470way_mammalian":{"rankscore":0.68203,"score":1.0}},"phylop":{"100way_vertebrate":{"rankscore":0.88732,"score":8.017},"17way_primate":{"rankscore":0.62972,"score":0.665},"470way_mammalian":{"rankscore":0.70487,"score":7.84}},"polyphen2":{"hdiv":{"pred":["D","D","D"],"rankscore":0.90584,"score":[1.0,1.0,1.0]},"hvar":{"pred":["D","D","D"],"rankscore":0.82059,"score":[0.994,0.977,0.994]}},"primateai":{"pred":"T","rankscore":0.70122,"score":0.720510363579},"provean":{"converted_rankscore":0.85921,"pred":["D","D","D"],"score":[-5.51,-5.41,-5.41]},"ref":"T","reliability_index":9,"revel":{"rankscore":0.93306,"score":[0.796,0.796,0.796]},"sift":{"converted_rankscore":0.91255,"pred":["D","D","D"],"score":[0.0,0.001,0.0]},"sift4g":{"converted_rankscore":0.83351,"pred":["D","D","D","D"],"score":[0.001,0.001,0.001,0.001]},"siphy_29way":{"logodds_rankscore":0.75989,"logodds_score":15.5613,"pi":{"a":0.0,"c":0.0,"g":0.0,"t":1.0}},"tsl":[1,1,1,1],"uniprot":[{"acc":"Q86TC9","entry":"MYPN_HUMAN"},{"acc":"Q86TC9-2","entry":"MYPN_HUMAN"},{"acc":"Q86TC9","entry":"MYPN_HUMAN"},{"acc":"A0A087WX60","entry":"A0A087WX60_HUMAN"}],"varity":{"er":{"rankscore":0.98189,"score":[0.9465644,0.9465644]},"er_loo":{"rankscore":0.98189,"score":[0.9465644,0.9465644]},"r":{"rankscore":0.9783,"score":[0.96551347,0.96551347]},"r_loo":{"rankscore":0.9783,"score":[0.96551347,0.96551347]}},"vep_canonical":"YES","vest4":{"rankscore":0.97643,"score":[0.966,0.96,0.957,0.949]},"vindijia_neandertal":["T","T"]},"hg38":{"end":68199393,"start":68199393},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"5711","position":"3498"},"cds":{"length":"3963","position":"3311"},"effect":"missense_variant","feature_id":"NM_001256267.1","feature_type":"transcript","gene_id":"MYPN","genename":"MYPN","hgvs_c":"c.3311T>C","hgvs_p":"p.Leu1104Pro","protein":{"length":"1320","position":"1104"},"putative_impact":"MODERATE","rank":"18","total":"21","transcript_biotype":"protein_coding"},{"cdna":{"length":"6120","position":"3907"},"cds":{"length":"3081","position":"2429"},"effect":"missense_variant","feature_id":"NM_001256268.1","feature_type":"transcript","gene_id":"MYPN","genename":"MYPN","hgvs_c":"c.2429T>C","hgvs_p":"p.Leu810Pro","protein":{"length":"1026","position":"810"},"putative_impact":"MODERATE","rank":"21","total":"24","transcript_biotype":"protein_coding"},{"cdna":{"length":"5816","position":"3603"},"cds":{"length":"3963","position":"3311"},"effect":"missense_variant","feature_id":"NM_032578.3","feature_type":"transcript","gene_id":"MYPN","genename":"MYPN","hgvs_c":"c.3311T>C","hgvs_p":"p.Leu1104Pro","protein":{"length":"1320","position":"1104"},"putative_impact":"MODERATE","rank":"17","total":"20","transcript_biotype":"protein_coding"},{"effect":"non_coding_transcript_exon_variant","feature_id":"NR_045662.3","feature_type":"transcript","gene_id":"MYPN","genename":"MYPN","hgvs_c":"n.2738T>C","putative_impact":"MODIFIER","rank":"17","total":"20","transcript_biotype":"pseudogene"},{"effect":"non_coding_transcript_exon_variant","feature_id":"NR_045663.3","feature_type":"transcript","gene_id":"MYPN","genename":"MYPN","hgvs_c":"n.3440T>C","putative_impact":"MODIFIER","rank":"15","total":"18","transcript_biotype":"pseudogene"}]},"vcf":{"alt":"C","position":"68199393","ref":"T"}}