{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA321053", "communityStandardTitle": [ "NM_005138.3(SCO2):c.283C>T (p.Arg95Cys)", "NM_152299.4(NCAPH2):c.*754G>A" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=3065983", "active": true, "id": "COSM3065983" }, { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=3065984", "active": true, "id": "COSM3065984" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=211966[alleleid]", "alleleId": 211966, "preferredName": "NM_005138.3(SCO2):c.283C>T (p.Arg95Cys)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1477832", "RCV": [ "RCV001971786" ], "variationId": 1477832 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/22-50962558-G-A", "id": "22-50962558-G-A", "variant": "22:50962558 G / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr22:g.50962558G>A?assembly=hg19", "id": "chr22:g.50962558G>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr22:g.50524129G>A?assembly=hg38", "id": "chr22:g.50524129G>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/748973032", "rs": 748973032 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/22-50962558-G-A?dataset=gnomad_r2_1", "id": "22-50962558-G-A", "variant": "22:50962558 G / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/22-50524129-G-A?dataset=gnomad_r4", "id": "22-50524129-G-A", "variant": "22:50524129 G / A" } ] }, "genomicAlleles": [ { "chromosome": "22", "coordinates": [ { "allele": "A", "end": 50524129, "referenceAllele": "G", "start": 50524128 } ], "hgvs": [ "NC_000022.11:g.50524129G>A", "CM000684.2:g.50524129G>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000070" }, { "chromosome": "22", "coordinates": [ { "allele": "A", "end": 50962558, "referenceAllele": "G", "start": 50962557 } ], "hgvs": [ "NC_000022.10:g.50962558G>A", "CM000684.1:g.50962558G>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000046" }, { "chromosome": "22", "coordinates": [ { "allele": "A", "end": 49309424, "referenceAllele": "G", "start": 49309423 } ], "hgvs": [ "NC_000022.9:g.49309424G>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000022" }, { "coordinates": [ { "allele": "T", "end": 10957, "referenceAllele": "C", "start": 10956 } ], "hgvs": [ "NG_011860.1:g.10957C>T", "LRG_727:g.10957C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS002037" }, { "coordinates": [ { "allele": "T", "end": 7311, "referenceAllele": "C", "start": 7310 } ], "hgvs": [ "NG_016235.1:g.7311C>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS003035" }, { "coordinates": [ { "allele": "A", "end": 20914, "referenceAllele": "G", "start": 20913 } ], "hgvs": [ "NG_021419.1:g.20914G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS003644" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 423, "referenceAllele": "C", "start": 422 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "ENST00000395693.8:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000379046.4:p.Arg95Cys", "hgvsWellDefined": "ENSP00000379046.4:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS753427", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000395693.8:c.283C>T" }, "RefSeq": { "hgvs": "NM_005138.3:c.283C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000379046.4:p.Arg95Cys" }, "RefSeq": { "hgvs": "NP_005129.2:p.Arg95Cys" } } } }, { "coordinates": [ { "allele": "A", "end": 2686, "referenceAllele": "G", "start": 2685 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "ENST00000420993.7:c.*754G>A" ], "proteinEffect": { "hgvs": "ENSP00000410088.2:n.*754G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS754864", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000420993.7:c.*754G>A" }, "RefSeq": { "hgvs": "NM_152299.4:c.*754G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000410088.2:n.*754G>A" }, "RefSeq": { "hgvs": "NP_689512.2:n.*754G>A" } } } }, { "coordinates": [ { "allele": "T", "end": 512, "referenceAllele": "C", "start": 511 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "ENST00000543927.6:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000444433.1:p.Arg95Cys", "hgvsWellDefined": "ENSP00000444433.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS759753" }, { "coordinates": [ { "allele": "T", "end": 441, "referenceAllele": "C", "start": 440 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "ENST00000638598.2:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000491753.2:p.Arg95Cys", "hgvsWellDefined": "ENSP00000491753.2:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS764608" }, { "coordinates": [ { "allele": "T", "end": 459, "referenceAllele": "C", "start": 458 } ], "hgvs": [ "ENST00000252785.3:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000252785.3:p.Arg95Cys", "hgvsWellDefined": "ENSP00000252785.3:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS249856" }, { "coordinates": [ { "allele": "T", "end": 431, "referenceAllele": "C", "start": 430 } ], "hgvs": [ "ENST00000395693.7:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000379046.3:p.Arg95Cys", "hgvsWellDefined": "ENSP00000379046.3:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS276837" }, { "coordinates": [ { "allele": "T", "end": 490, "referenceAllele": "C", "start": 489 } ], "hgvs": [ "ENST00000423348.1:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000403570.1:p.Arg95Cys", "hgvsWellDefined": "ENSP00000403570.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS287717" }, { "coordinates": [ { "allele": "T", "end": 441, "referenceAllele": "C", "start": 440 } ], "hgvs": [ "ENST00000439934.5:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000415642.1:p.Arg95Cys", "hgvsWellDefined": "ENSP00000415642.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS295651" }, { "coordinates": [ { "allele": "T", "end": 441, "referenceAllele": "C", "start": 440 } ], "hgvs": [ "ENST00000535425.5:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000444242.1:p.Arg95Cys", "hgvsWellDefined": "ENSP00000444242.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS359724" }, { "coordinates": [ { "allele": "T", "end": 490, "referenceAllele": "C", "start": 489 } ], "hgvs": [ "ENST00000543927.5:c.283C>T" ], "proteinEffect": { "hgvs": "ENSP00000444433.1:p.Arg95Cys", "hgvsWellDefined": "ENSP00000444433.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS364285" }, { "@id": "http://reg.genome.network/allele/PA321054", "coordinates": [ { "allele": "T", "end": 490, "referenceAllele": "C", "start": 489 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_001169109.1:c.283C>T" ], "proteinEffect": { "hgvs": "NP_001162580.1:p.Arg95Cys", "hgvsWellDefined": "NP_001162580.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS015144" }, { "@id": "http://reg.genome.network/allele/PA2826059355", "coordinates": [ { "allele": "T", "end": 441, "referenceAllele": "C", "start": 440 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_001169110.1:c.283C>T" ], "proteinEffect": { "hgvs": "NP_001162581.1:p.Arg95Cys", "hgvsWellDefined": "NP_001162581.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS015145" }, { "@id": "http://reg.genome.network/allele/PA2826059652", "coordinates": [ { "allele": "T", "end": 459, "referenceAllele": "C", "start": 458 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_001169111.1:c.283C>T" ], "proteinEffect": { "hgvs": "NP_001162582.1:p.Arg95Cys", "hgvsWellDefined": "NP_001162582.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS015146" }, { "coordinates": [ { "allele": "A", "end": 2697, "referenceAllele": "G", "start": 2696 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "NM_001185011.1:c.*754G>A" ], "proteinEffect": { "hgvs": "NP_001171940.1:n.*754G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS016080" }, { "@id": "http://reg.genome.network/allele/PA321055", "coordinates": [ { "allele": "T", "end": 430, "referenceAllele": "C", "start": 429 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_005138.2:c.283C>T" ], "proteinEffect": { "hgvs": "NP_005129.2:p.Arg95Cys", "hgvsWellDefined": "NP_005129.2:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS030259" }, { "coordinates": [ { "allele": "A", "end": 2694, "referenceAllele": "G", "start": 2693 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "NM_152299.3:c.*754G>A" ], "proteinEffect": { "hgvs": "NP_689512.2:n.*754G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS041761" }, { "coordinates": [ { "allele": "A", "end": 2782, "referenceAllele": "G", "start": 2781 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "XR_001755232.1:n.2782G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS601066" }, { "coordinates": [ { "allele": "A", "end": 2686, "referenceAllele": "G", "start": 2685 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "NM_152299.4:c.*754G>A" ], "proteinEffect": { "hgvs": "NP_689512.2:n.*754G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS672276", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000420993.7:c.*754G>A" }, "RefSeq": { "hgvs": "NM_152299.4:c.*754G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000410088.2:n.*754G>A" }, "RefSeq": { "hgvs": "NP_689512.2:n.*754G>A" } } } }, { "coordinates": [ { "allele": "A", "end": 2689, "referenceAllele": "G", "start": 2688 } ], "gene": "http://reg.genome.network/gene/GN025071", "geneNCBI_id": 29781, "geneSymbol": "NCAPH2", "hgvs": [ "NM_001185011.2:c.*754G>A" ], "proteinEffect": { "hgvs": "NP_001171940.1:n.*754G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS679060" }, { "@id": "http://reg.genome.network/allele/PA321055", "coordinates": [ { "allele": "T", "end": 423, "referenceAllele": "C", "start": 422 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_005138.3:c.283C>T" ], "proteinEffect": { "hgvs": "NP_005129.2:p.Arg95Cys", "hgvsWellDefined": "NP_005129.2:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS696334", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000395693.8:c.283C>T" }, "RefSeq": { "hgvs": "NM_005138.3:c.283C>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000379046.4:p.Arg95Cys" }, "RefSeq": { "hgvs": "NP_005129.2:p.Arg95Cys" } } } }, { "@id": "http://reg.genome.network/allele/PA321054", "coordinates": [ { "allele": "T", "end": 493, "referenceAllele": "C", "start": 492 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_001169109.2:c.283C>T" ], "proteinEffect": { "hgvs": "NP_001162580.1:p.Arg95Cys", "hgvsWellDefined": "NP_001162580.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS713304" }, { "@id": "http://reg.genome.network/allele/PA2826059652", "coordinates": [ { "allele": "T", "end": 453, "referenceAllele": "C", "start": 452 } ], "gene": "http://reg.genome.network/gene/GN010604", "geneNCBI_id": 9997, "geneSymbol": "SCO2", "hgvs": [ "NM_001169111.2:c.283C>T" ], "proteinEffect": { "hgvs": "NP_001162582.1:p.Arg95Cys", "hgvsWellDefined": "NP_001162582.1:p.Arg95Cys" }, "referenceSequence": "http://reg.genome.network/refseq/RS713305" } ], "type": "nucleotide" }