{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA000407", "communityStandardTitle": [ "NM_000314.8(PTEN):c.347_351del (p.Asp116AlafsTer8)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=22857[alleleid]", "alleleId": 22857, "preferredName": "NM_000314.8(PTEN):c.347_351del (p.Asp116fs)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/7818", "RCV": [ "RCV000008262", "RCV000460680" ], "variationId": 7818 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.89692863_89692867del?assembly=hg19", "id": "chr10:g.89692863_89692867del" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr10:g.87933106_87933110del?assembly=hg38", "id": "chr10:g.87933106_87933110del" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/587776666", "rs": 587776666 } ] }, "genomicAlleles": [ { "chromosome": "10", "coordinates": [ { "allele": "", "end": 87933110, "referenceAllele": "ACAAT", "start": 87933105 } ], "hgvs": [ "NC_000010.11:g.87933106_87933110del", "CM000672.2:g.87933106_87933110del" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000058" }, { "chromosome": "10", "coordinates": [ { "allele": "", "end": 89692867, "referenceAllele": "ACAAT", "start": 89692862 } ], "hgvs": [ "NC_000010.10:g.89692863_89692867del", "CM000672.1:g.89692863_89692867del" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000034" }, { "chromosome": "10", "coordinates": [ { "allele": "", "end": 89682847, "referenceAllele": "ACAAT", "start": 89682842 } ], "hgvs": [ "NC_000010.9:g.89682843_89682847del" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000010" }, { "coordinates": [ { "allele": "", "end": 74672, "referenceAllele": "ACAAT", "start": 74667 } ], "hgvs": [ "NG_007466.2:g.74668_74672del", "LRG_311:g.74668_74672del" ], "referenceSequence": "http://reg.genome.network/refseq/RS000591" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "", "end": 1196, "referenceAllele": "ACAAT", "start": 1191 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.2:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000514759.2:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000514759.2:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS914478" }, { "coordinates": [ { "allele": "", "end": 1196, "referenceAllele": "ACAAT", "start": 1191 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000710265.1:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000518161.1:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000518161.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS914503" }, { "coordinates": [ { "allele": "", "end": 492, "referenceAllele": "ACAAT", "start": 487 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000472832.3:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000483066.2:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000483066.2:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS905199" }, { "coordinates": [ { "allele": "", "end": 1086, "referenceAllele": "ACAAT", "start": 1081 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.2:n.1082_1086del" ], "referenceSequence": "http://reg.genome.network/refseq/RS906571" }, { "coordinates": [ { "allele": "", "end": 544, "referenceAllele": "ACAAT", "start": 539 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.2:c.*177_*181del" ], "proteinEffect": { "hgvs": "ENSP00000508742.2:n.*177_*181del" }, "referenceSequence": "http://reg.genome.network/refseq/RS906576" }, { "coordinates": [ { "allele": "", "end": 981, "referenceAllele": "ACAAT", "start": 976 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700021.1:c.302_306del" ], "proteinEffect": { "hgvs": "ENSP00000514757.1:p.Asp101AlafsTer8", "hgvsWellDefined": "ENSP00000514757.1:p.[Asp101_Val104del;Ala106_His108del;Lys110_Ile120del;Ala122_Leu124delinsSerAsnSer;His126_Lys132del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS910887" }, { "coordinates": [ { "allele": "", "end": 742, "referenceAllele": "ACAAT", "start": 737 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700022.1:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000514758.1:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000514758.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS910888" }, { "coordinates": [ { "allele": "", "end": 185, "referenceAllele": "ACAAT", "start": 180 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000700029.1:c.181_185del" ], "referenceSequence": "http://reg.genome.network/refseq/RS910893" }, { "coordinates": [ { "allele": "", "end": 447, "referenceAllele": "ACAAT", "start": 442 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706954.1:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000516674.1:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000516674.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS913291" }, { "coordinates": [ { "allele": "", "end": 1366, "referenceAllele": "ACAAT", "start": 1361 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000706955.1:c.*382_*386del" ], "proteinEffect": { "hgvs": "ENSP00000516675.1:n.*382_*386del" }, "referenceSequence": "http://reg.genome.network/refseq/RS913292" }, { "coordinates": [ { "allele": "", "end": 493, "referenceAllele": "ACAAT", "start": 488 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000686459.1:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000508909.1:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000508909.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS830588" }, { "coordinates": [ { "allele": "", "end": 1442, "referenceAllele": "ACAAT", "start": 1437 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688158.1:c.*458_*462del" ], "proteinEffect": { "hgvs": "ENSP00000509254.1:n.*458_*462del" }, "referenceSequence": "http://reg.genome.network/refseq/RS831470" }, { "coordinates": [ { "allele": "", "end": 843, "referenceAllele": "ACAAT", "start": 838 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688308.1:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000508752.1:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000508752.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS831553" }, { "coordinates": [ { "allele": "", "end": 272, "referenceAllele": "ACAAT", "start": 267 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000688922.1:c.268_272del" ], "referenceSequence": "http://reg.genome.network/refseq/RS831892" }, { "coordinates": [ { "allele": "", "end": 1382, "referenceAllele": "ACAAT", "start": 1377 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000693560.1:c.866_870del" ], "proteinEffect": { "hgvs": "ENSP00000509861.1:p.Asp289AlafsTer8", "hgvsWellDefined": "ENSP00000509861.1:p.[Asp289_Val292del;Ala294_His296del;Lys298_Ile308del;Ala310_Leu312delinsSerAsnSer;His314_Lys320del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS834309" }, { "coordinates": [ { "allele": "", "end": 1196, "referenceAllele": "ACAAT", "start": 1191 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.8:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000361021.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS750898", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.347_351del" }, "RefSeq": { "hgvs": "NM_000314.8:c.347_351del" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Asp116AlafsTer8" }, "RefSeq": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8" } } } }, { "coordinates": [ { "allele": "", "end": 1708, "referenceAllele": "ACAAT", "start": 1703 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000371953.7:c.347_351del" ], "proteinEffect": { "hgvs": "ENSP00000361021.3:p.Asp116AlafsTer8", "hgvsWellDefined": "ENSP00000361021.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS247170" }, { "coordinates": [ { "allele": "", "end": 177, "referenceAllele": "ACAAT", "start": 172 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000498703.1:n.173_177del" ], "referenceSequence": "http://reg.genome.network/refseq/RS334650" }, { "coordinates": [ { "allele": "", "end": 1383, "referenceAllele": "ACAAT", "start": 1378 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "ENST00000610634.1:c.245_249del" ], "proteinEffect": { "hgvs": "ENSP00000477517.1:p.Asp82AlafsTer8", "hgvsWellDefined": "ENSP00000477517.1:p.[Asp82_Val85del;Ala87_His89del;Lys91_Ile101del;Ala103_Leu105delinsSerAsnSer;His107_Lys113del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS400508" }, { "coordinates": [ { "allele": "", "end": 1382, "referenceAllele": "ACAAT", "start": 1377 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.5:c.347_351del" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8", "hgvsWellDefined": "NP_000305.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS006376" }, { "coordinates": [ { "allele": "", "end": 1382, "referenceAllele": "ACAAT", "start": 1377 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.6:c.347_351del" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8", "hgvsWellDefined": "NP_000305.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS006377" }, { "coordinates": [ { "allele": "", "end": 1382, "referenceAllele": "ACAAT", "start": 1377 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.2:c.866_870del" ], "proteinEffect": { "hgvs": "NP_001291646.2:p.Asp289AlafsTer8", "hgvsWellDefined": "NP_001291646.2:p.[Asp289_Val292del;Ala294_His296del;Lys298_Ile308del;Ala310_Leu312delinsSerAsnSer;His314_Lys320del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS025775" }, { "coordinates": [ { "allele": "", "end": 1337, "referenceAllele": "ACAAT", "start": 1332 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.1:c.-404_-400del" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-404_-400del" }, "referenceSequence": "http://reg.genome.network/refseq/RS025776" }, { "coordinates": [ { "allele": "", "end": 1018, "referenceAllele": "ACAAT", "start": 1013 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_006717926.2:c.302_306del" ], "proteinEffect": { "hgvs": "XP_006717989.1:p.Asp101AlafsTer8", "hgvsWellDefined": "XP_006717989.1:p.[Asp101_Val104del;Ala106_His108del;Lys110_Ile120del;Ala122_Leu124delinsSerAsnSer;His126_Lys132del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS072385" }, { "coordinates": [ { "allele": "", "end": 1063, "referenceAllele": "ACAAT", "start": 1058 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539981.1:c.347_351del" ], "proteinEffect": { "hgvs": "XP_011538283.1:p.Asp116AlafsTer8", "hgvsWellDefined": "XP_011538283.1:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS106931" }, { "coordinates": [ { "allele": "", "end": 4035, "referenceAllele": "ACAAT", "start": 4030 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XM_011539982.1:c.251_255del" ], "proteinEffect": { "hgvs": "XP_011538284.1:p.Asp84AlafsTer8", "hgvsWellDefined": "XP_011538284.1:p.[Asp84_Val87del;Ala89_His91del;Lys93_Ile103del;Ala105_Leu107delinsSerAsnSer;His109_Lys115del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS106932" }, { "coordinates": [ { "allele": "", "end": 1063, "referenceAllele": "ACAAT", "start": 1058 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945789.1:n.1059_1063del" ], "referenceSequence": "http://reg.genome.network/refseq/RS139422" }, { "coordinates": [ { "allele": "", "end": 1063, "referenceAllele": "ACAAT", "start": 1058 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945790.1:n.1059_1063del" ], "referenceSequence": "http://reg.genome.network/refseq/RS139423" }, { "coordinates": [ { "allele": "", "end": 1063, "referenceAllele": "ACAAT", "start": 1058 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "XR_945791.1:n.1059_1063del" ], "referenceSequence": "http://reg.genome.network/refseq/RS139424" }, { "coordinates": [ { "allele": "", "end": 1195, "referenceAllele": "ACAAT", "start": 1190 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.7:c.347_351del" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8", "hgvsWellDefined": "NP_000305.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS662397" }, { "coordinates": [ { "allele": "", "end": 1195, "referenceAllele": "ACAAT", "start": 1190 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304717.5:c.866_870del" ], "proteinEffect": { "hgvs": "NP_001291646.4:p.Asp289AlafsTer8", "hgvsWellDefined": "NP_001291646.4:p.[Asp289_Val292del;Ala294_His296del;Lys298_Ile308del;Ala310_Leu312delinsSerAsnSer;His314_Lys320del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS664314" }, { "coordinates": [ { "allele": "", "end": 1150, "referenceAllele": "ACAAT", "start": 1145 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_001304718.2:c.-404_-400del" ], "proteinEffect": { "hgvs": "NP_001291647.1:n.-404_-400del" }, "referenceSequence": "http://reg.genome.network/refseq/RS664315" }, { "coordinates": [ { "allele": "", "end": 1196, "referenceAllele": "ACAAT", "start": 1191 } ], "gene": "http://reg.genome.network/gene/GN009588", "geneNCBI_id": 5728, "geneSymbol": "PTEN", "hgvs": [ "NM_000314.8:c.347_351del" ], "proteinEffect": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8", "hgvsWellDefined": "NP_000305.3:p.[Asp116_Val119del;Ala121_His123del;Lys125_Ile135del;Ala137_Leu139delinsSerAsnSer;His141_Lys147del]" }, "referenceSequence": "http://reg.genome.network/refseq/RS674788", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000371953.8:c.347_351del" }, "RefSeq": { "hgvs": "NM_000314.8:c.347_351del" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000361021.3:p.Asp116AlafsTer8" }, "RefSeq": { "hgvs": "NP_000305.3:p.Asp116AlafsTer8" } } } } ], "type": "nucleotide" }