{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA384540524", "communityStandardTitle": [ "NM_001844.5(COL2A1):c.3149G>A (p.Gly1050Asp)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=492657[alleleid]", "alleleId": 492657, "preferredName": "NM_001844.5(COL2A1):c.3149G>A (p.Gly1050Asp)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/501233", "RCV": [ "RCV000593974", "RCV001822860" ], "variationId": 501233 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.48371399C>T?assembly=hg19", "id": "chr12:g.48371399C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.47977616C>T?assembly=hg38", "id": "chr12:g.47977616C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1555165242", "rs": 1555165242 } ] }, "genomicAlleles": [ { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 47977616, "referenceAllele": "C", "start": 47977615 } ], "hgvs": [ "NC_000012.12:g.47977616C>T", "CM000674.2:g.47977616C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000060" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 48371399, "referenceAllele": "C", "start": 48371398 } ], "hgvs": [ "NC_000012.11:g.48371399C>T", "CM000674.1:g.48371399C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000036" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 46657666, "referenceAllele": "C", "start": 46657665 } ], "hgvs": [ "NC_000012.10:g.46657666C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000012" }, { "coordinates": [ { "allele": "A", "end": 31887, "referenceAllele": "G", "start": 31886 } ], "hgvs": [ "NG_008072.1:g.31887G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000817" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 3127, "referenceAllele": "G", "start": 3126 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.7:c.2942G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly981Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly981Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS747643" }, { "coordinates": [ { "allele": "A", "end": 3304, "referenceAllele": "G", "start": 3303 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.8:c.3149G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly1050Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly1050Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS752395", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.3149G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.3149G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly1050Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly1050Asp" } } } }, { "coordinates": [ { "allele": "A", "end": 2942, "referenceAllele": "G", "start": 2941 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.6:c.2942G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly981Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly981Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS260445" }, { "coordinates": [ { "allele": "A", "end": 3314, "referenceAllele": "G", "start": 3313 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.7:c.3149G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly1050Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly1050Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS272956" }, { "coordinates": [ { "allele": "A", "end": 2235, "referenceAllele": "G", "start": 2234 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000493991.5:n.2235G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS331026" }, { "@id": "http://reg.genome.network/allele/PA658810251", "coordinates": [ { "allele": "A", "end": 3330, "referenceAllele": "G", "start": 3329 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.4:c.3149G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly1050Asp", "hgvsWellDefined": "NP_001835.3:p.Gly1050Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS027172" }, { "@id": "http://reg.genome.network/allele/PA916076379", "coordinates": [ { "allele": "A", "end": 3123, "referenceAllele": "G", "start": 3122 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.2:c.2942G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly981Asp", "hgvsWellDefined": "NP_149162.2:p.Gly981Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS039568" }, { "coordinates": [ { "allele": "A", "end": 3882, "referenceAllele": "G", "start": 3881 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_006719242.2:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_006719305.2:p.Gly1098Asp", "hgvsWellDefined": "XP_006719305.2:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS073018" }, { "coordinates": [ { "allele": "A", "end": 4059, "referenceAllele": "G", "start": 4058 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537928.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536230.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536230.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104886" }, { "coordinates": [ { "allele": "A", "end": 3650, "referenceAllele": "G", "start": 3649 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537929.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536231.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536231.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104887" }, { "coordinates": [ { "allele": "A", "end": 3651, "referenceAllele": "G", "start": 3650 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537930.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536232.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536232.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104888" }, { "coordinates": [ { "allele": "A", "end": 3633, "referenceAllele": "G", "start": 3632 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537931.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536233.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536233.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104889" }, { "coordinates": [ { "allele": "A", "end": 3977, "referenceAllele": "G", "start": 3976 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537932.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536234.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536234.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104890" }, { "coordinates": [ { "allele": "A", "end": 3611, "referenceAllele": "G", "start": 3610 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537933.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_011536235.1:p.Gly1098Asp", "hgvsWellDefined": "XP_011536235.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104891" }, { "coordinates": [ { "allele": "A", "end": 4056, "referenceAllele": "G", "start": 4055 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537934.1:c.3290G>A" ], "proteinEffect": { "hgvs": "XP_011536236.1:p.Gly1097Asp", "hgvsWellDefined": "XP_011536236.1:p.Gly1097Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104892" }, { "coordinates": [ { "allele": "A", "end": 2585, "referenceAllele": "G", "start": 2584 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537935.1:c.2237G>A" ], "proteinEffect": { "hgvs": "XP_011536237.1:p.Gly746Asp", "hgvsWellDefined": "XP_011536237.1:p.Gly746Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104893" }, { "coordinates": [ { "allele": "A", "end": 3415, "referenceAllele": "G", "start": 3414 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018828.1:c.3293G>A" ], "proteinEffect": { "hgvs": "XP_016874317.1:p.Gly1098Asp", "hgvsWellDefined": "XP_016874317.1:p.Gly1098Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570670" }, { "coordinates": [ { "allele": "A", "end": 3412, "referenceAllele": "G", "start": 3411 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018829.1:c.3290G>A" ], "proteinEffect": { "hgvs": "XP_016874318.1:p.Gly1097Asp", "hgvsWellDefined": "XP_016874318.1:p.Gly1097Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570671" }, { "coordinates": [ { "allele": "A", "end": 3205, "referenceAllele": "G", "start": 3204 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018830.1:c.3083G>A" ], "proteinEffect": { "hgvs": "XP_016874319.1:p.Gly1028Asp", "hgvsWellDefined": "XP_016874319.1:p.Gly1028Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570672" }, { "coordinates": [ { "allele": "A", "end": 3638, "referenceAllele": "G", "start": 3637 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018831.2:c.2603G>A" ], "proteinEffect": { "hgvs": "XP_016874320.1:p.Gly868Asp", "hgvsWellDefined": "XP_016874320.1:p.Gly868Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570673" }, { "@id": "http://reg.genome.network/allele/PA658810251", "coordinates": [ { "allele": "A", "end": 3304, "referenceAllele": "G", "start": 3303 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.5:c.3149G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly1050Asp", "hgvsWellDefined": "NP_001835.3:p.Gly1050Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS665206", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.3149G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.3149G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly1050Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly1050Asp" } } } }, { "@id": "http://reg.genome.network/allele/PA916076379", "coordinates": [ { "allele": "A", "end": 3097, "referenceAllele": "G", "start": 3096 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.3:c.2942G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly981Asp", "hgvsWellDefined": "NP_149162.2:p.Gly981Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS699283" } ], "type": "nucleotide" }