{"_id":"chr7:g.55191730C>A","_version":1,"chrom":"7","clingen":{"caid":"CA367580087"},"dbnsfp":{"_license":"http://bit.ly/2VLnQBz","aa":{"alt":"X","codon_degeneracy":[2,2,2],"codonpos":[3,3,3],"pos":[782,782,827],"ref":"Y","refcodon":["TAC","TAC","TAC"]},"aloft":{"confidence":"High","fraction_transcripts_affected":"3/7","pred":"Dominant","prob_dominant":"0.79815","prob_recessive":"0.1945","prob_tolerant":"0.00735"},"alt":"A","altai_neandertal":["C","C"],"ancestral_allele":"C","appris":"principal1","bayesdel":{"add_af":{"pred":"D","rankscore":0.99412,"score":0.625005},"no_af":{"pred":"D","rankscore":0.99401,"score":0.66}},"bstatistic":{"converted_rankscore":0.24599,"score":900.0},"cadd":{"phred":39.0,"raw_rankscore":0.98412,"raw_score":9.063916},"cds_strand":["+","+","+"],"chagyrskaya_neandertal":["C","C"],"chrom":"7","dann":{"rankscore":0.83927,"score":0.9974659656063761},"denisova":["C","C"],"eigen":{"phred_coding":7.151909,"raw_coding":0.70234608453946,"raw_coding_rankscore":0.79786},"eigen-pc":{"phred_coding":5.926061,"raw_coding":0.575175362098361,"raw_coding_rankscore":0.73164},"ensembl":{"geneid":["ENSG00000146648","ENSG00000146648","ENSG00000146648"],"proteinid":["ENSP00000415559","ENSP00000395243","ENSP00000275493"],"transcriptid":["ENST00000455089","ENST00000454757","ENST00000275493"]},"fathmm-mkl":{"coding_group":"AEFDBI","coding_pred":"D","coding_rankscore":0.54641,"coding_score":0.91962},"fathmm-xf":{"coding_pred":"N","coding_rankscore":0.39108,"coding_score":0.276314},"fitcons":{"gm12878":{"confidence_value":0,"rankscore":0.26702,"score":0.573888},"h1-hesc":{"confidence_value":0,"rankscore":0.30282,"score":0.584781},"huvec":{"confidence_value":0,"rankscore":0.65921,"score":0.6691},"integrated":{"confidence_value":0,"rankscore":0.48532,"score":0.653281}},"gencode_basic":["Y","Y","Y"],"genename":["EGFR","EGFR","EGFR"],"genocanyon":{"rankscore":0.74766,"score":0.99999993321866},"gerp":{"91_mammals":{"rankscore":0.55828,"score":3.06}},"gerp++":{"nr":5.82,"rs":4.94,"rs_rankscore":0.64645},"hg18":{"end":55226917,"start":55226917},"hg19":{"end":55259423,"start":55259423},"hg38":{"end":55191730,"start":55191730},"hgvsc":["c.2481C>A","c.2346C>A"],"hgvsp":["p.Tyr782*","p.Tyr782Ter","p.Tyr827*","p.Tyr827Ter","p.Y782X","p.Y827X"],"interpro":{"domain":["Serine-threonine/tyrosine-protein kinase, catalytic domain|Serine-threonine/tyrosine-protein kinase, catalytic domain|Protein kinase domain|Tyrosine-protein kinase, catalytic domain","Serine-threonine/tyrosine-protein kinase, catalytic domain|Serine-threonine/tyrosine-protein kinase, catalytic domain|Protein kinase domain|Tyrosine-protein kinase, catalytic domain","Serine-threonine/tyrosine-protein kinase, catalytic domain|Serine-threonine/tyrosine-protein kinase, catalytic domain|Protein kinase domain|Tyrosine-protein kinase, catalytic domain"]},"lrt":{"converted_rankscore":0.8433,"omega":0.0,"pred":"D","score":0.0},"mutationtaster":{"aae":["Y774*","Y827*","Y782*"],"converted_rankscore":0.81001,"model":["complex_aae","complex_aae","complex_aae","without_aae"],"pred":["A","A","A","D"],"score":[1.0,1.0,1.0,1.0]},"phastcons":{"100way_vertebrate":{"rankscore":0.3938,"score":0.996},"17way_primate":{"rankscore":0.71098,"score":0.994},"470way_mammalian":{"rankscore":0.31684,"score":0.992}},"phylop":{"100way_vertebrate":{"rankscore":0.26309,"score":0.772},"17way_primate":{"rankscore":0.4025,"score":0.599},"470way_mammalian":{"rankscore":0.17857,"score":0.388}},"ref":"C","siphy_29way":{"logodds_rankscore":0.39943,"logodds_score":9.8027,"pi":{"a":0.0,"c":0.8434,"g":0.0,"t":0.1566}},"tsl":[1,1,1],"uniprot":[{"acc":"Q504U8","entry":"Q504U8_HUMAN"},{"acc":"E9PFD7","entry":"E9PFD7_HUMAN"},{"acc":"P00533","entry":"EGFR_HUMAN"}],"vep_canonical":"YES","vest4":{"rankscore":0.96984,"score":[0.947,0.944,0.96]},"vindijia_neandertal":["C","C"]},"hg38":{"end":55191730,"start":55191730},"observed":true,"snpeff":{"_license":"http://bit.ly/2suyRKt","ann":[{"cdna":{"length":"5600","position":"2727"},"cds":{"length":"3633","position":"2481"},"effect":"stop_gained","feature_id":"NM_005228.3","feature_type":"transcript","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","hgvs_p":"p.Tyr827*","protein":{"length":"1210","position":"827"},"putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"1XKK:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2EB2:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2EB3:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITN:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITP:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITQ:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITT:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITU:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITV:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITW:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITX:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2ITZ:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2J5F:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"2RGP:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3BEL:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3IKA:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3IKA:B_770-B_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3POZ:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3UG1:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3UG2:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3VJN:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3VJO:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W2O:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W2P:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W2Q:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W2R:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W2S:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W32:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"3W33:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4I1Z:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4I22:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4I23:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4I24:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4I24:B_770-B_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4LI5:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4LQM:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4R5S:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4RJ4:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4RJ6:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4RJ7:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4RJ8:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4WKQ:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"effect":"structural_interaction_variant","feature_id":"4WRG:A_770-A_827:NM_005228.3","feature_type":"interaction","gene_id":"EGFR","genename":"EGFR","hgvs_c":"c.2481C>A","putative_impact":"HIGH","rank":"21","total":"28","transcript_biotype":"protein_coding"},{"distance_to_feature":"2781","effect":"upstream_gene_variant","feature_id":"NR_047551.1","feature_type":"transcript","gene_id":"EGFR-AS1","genename":"EGFR-AS1","hgvs_c":"n.-2781G>T","putative_impact":"MODIFIER","transcript_biotype":"pseudogene"}],"lof":{"gene_id":"EGFR","genename":"EGFR","number_of_transcripts_in_gene":"4","percent_of_transcripts_affected":"0.25"},"nmd":{"gene_id":"EGFR","genename":"EGFR","number_of_transcripts_in_gene":"4","percent_of_transcripts_affected":"0.25"}},"vcf":{"alt":"A","position":"55191730","ref":"C"}}