{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA127160", "communityStandardTitle": [ "NM_001844.5(COL2A1):c.908G>A (p.Gly303Asp)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=32409[alleleid]", "alleleId": 32409, "preferredName": "NM_001844.5(COL2A1):c.908G>A (p.Gly303Asp)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/17370", "RCV": [ "RCV000018914", "RCV000724305" ], "variationId": 17370 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.48387608C>T?assembly=hg19", "id": "chr12:g.48387608C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.47993825C>T?assembly=hg38", "id": "chr12:g.47993825C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/121912877", "rs": 121912877 } ] }, "genomicAlleles": [ { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 47993825, "referenceAllele": "C", "start": 47993824 } ], "hgvs": [ "NC_000012.12:g.47993825C>T", "CM000674.2:g.47993825C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000060" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 48387608, "referenceAllele": "C", "start": 48387607 } ], "hgvs": [ "NC_000012.11:g.48387608C>T", "CM000674.1:g.48387608C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000036" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 46673875, "referenceAllele": "C", "start": 46673874 } ], "hgvs": [ "NC_000012.10:g.46673875C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000012" }, { "coordinates": [ { "allele": "A", "end": 15678, "referenceAllele": "G", "start": 15677 } ], "hgvs": [ "NG_008072.1:g.15678G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000817" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 886, "referenceAllele": "G", "start": 885 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.7:c.701G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly234Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly234Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS747643" }, { "coordinates": [ { "allele": "A", "end": 1063, "referenceAllele": "G", "start": 1062 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.8:c.908G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly303Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly303Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS752395", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.908G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.908G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly303Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly303Asp" } } } }, { "coordinates": [ { "allele": "A", "end": 701, "referenceAllele": "G", "start": 700 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.6:c.701G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly234Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly234Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS260445" }, { "coordinates": [ { "allele": "A", "end": 1073, "referenceAllele": "G", "start": 1072 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.7:c.908G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly303Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly303Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS272956" }, { "@id": "http://reg.genome.network/allele/PA098010", "coordinates": [ { "allele": "A", "end": 1089, "referenceAllele": "G", "start": 1088 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.4:c.908G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly303Asp", "hgvsWellDefined": "NP_001835.3:p.Gly303Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS027172" }, { "@id": "http://reg.genome.network/allele/PA127161", "coordinates": [ { "allele": "A", "end": 882, "referenceAllele": "G", "start": 881 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.2:c.701G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly234Asp", "hgvsWellDefined": "NP_149162.2:p.Gly234Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS039568" }, { "coordinates": [ { "allele": "A", "end": 1641, "referenceAllele": "G", "start": 1640 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_006719242.2:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_006719305.2:p.Gly351Asp", "hgvsWellDefined": "XP_006719305.2:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS073018" }, { "coordinates": [ { "allele": "A", "end": 1818, "referenceAllele": "G", "start": 1817 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537928.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536230.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536230.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104886" }, { "coordinates": [ { "allele": "A", "end": 1409, "referenceAllele": "G", "start": 1408 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537929.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536231.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536231.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104887" }, { "coordinates": [ { "allele": "A", "end": 1410, "referenceAllele": "G", "start": 1409 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537930.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536232.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536232.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104888" }, { "coordinates": [ { "allele": "A", "end": 1392, "referenceAllele": "G", "start": 1391 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537931.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536233.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536233.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104889" }, { "coordinates": [ { "allele": "A", "end": 1736, "referenceAllele": "G", "start": 1735 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537932.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536234.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536234.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104890" }, { "coordinates": [ { "allele": "A", "end": 1370, "referenceAllele": "G", "start": 1369 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537933.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_011536235.1:p.Gly351Asp", "hgvsWellDefined": "XP_011536235.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104891" }, { "coordinates": [ { "allele": "A", "end": 1815, "referenceAllele": "G", "start": 1814 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537934.1:c.1049G>A" ], "proteinEffect": { "hgvs": "XP_011536236.1:p.Gly350Asp", "hgvsWellDefined": "XP_011536236.1:p.Gly350Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104892" }, { "coordinates": [ { "allele": "A", "end": 1174, "referenceAllele": "G", "start": 1173 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018828.1:c.1052G>A" ], "proteinEffect": { "hgvs": "XP_016874317.1:p.Gly351Asp", "hgvsWellDefined": "XP_016874317.1:p.Gly351Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570670" }, { "coordinates": [ { "allele": "A", "end": 1171, "referenceAllele": "G", "start": 1170 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018829.1:c.1049G>A" ], "proteinEffect": { "hgvs": "XP_016874318.1:p.Gly350Asp", "hgvsWellDefined": "XP_016874318.1:p.Gly350Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570671" }, { "coordinates": [ { "allele": "A", "end": 964, "referenceAllele": "G", "start": 963 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018830.1:c.842G>A" ], "proteinEffect": { "hgvs": "XP_016874319.1:p.Gly281Asp", "hgvsWellDefined": "XP_016874319.1:p.Gly281Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570672" }, { "coordinates": [ { "allele": "A", "end": 1397, "referenceAllele": "G", "start": 1396 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018831.2:c.362G>A" ], "proteinEffect": { "hgvs": "XP_016874320.1:p.Gly121Asp", "hgvsWellDefined": "XP_016874320.1:p.Gly121Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570673" }, { "@id": "http://reg.genome.network/allele/PA098010", "coordinates": [ { "allele": "A", "end": 1063, "referenceAllele": "G", "start": 1062 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.5:c.908G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly303Asp", "hgvsWellDefined": "NP_001835.3:p.Gly303Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS665206", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.908G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.908G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly303Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly303Asp" } } } }, { "@id": "http://reg.genome.network/allele/PA127161", "coordinates": [ { "allele": "A", "end": 856, "referenceAllele": "G", "start": 855 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.3:c.701G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly234Asp", "hgvsWellDefined": "NP_149162.2:p.Gly234Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS699283" } ], "type": "nucleotide" }