{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA16619530", "communityStandardTitle": [ "NM_001844.5(COL2A1):c.647G>A (p.Gly216Asp)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=408666[alleleid]", "alleleId": 408666, "preferredName": "NM_001844.5(COL2A1):c.647G>A (p.Gly216Asp)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/420058", "RCV": [ "RCV000484205" ], "variationId": 420058 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.48389665C>T?assembly=hg19", "id": "chr12:g.48389665C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr12:g.47995882C>T?assembly=hg38", "id": "chr12:g.47995882C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1064794264", "rs": 1064794264 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/12-47995882-C-T?dataset=gnomad_r4", "id": "12-47995882-C-T", "variant": "12:47995882 C / T" } ] }, "genomicAlleles": [ { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 47995882, "referenceAllele": "C", "start": 47995881 } ], "hgvs": [ "NC_000012.12:g.47995882C>T", "CM000674.2:g.47995882C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000060" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 48389665, "referenceAllele": "C", "start": 48389664 } ], "hgvs": [ "NC_000012.11:g.48389665C>T", "CM000674.1:g.48389665C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000036" }, { "chromosome": "12", "coordinates": [ { "allele": "T", "end": 46675932, "referenceAllele": "C", "start": 46675931 } ], "hgvs": [ "NC_000012.10:g.46675932C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000012" }, { "coordinates": [ { "allele": "A", "end": 13621, "referenceAllele": "G", "start": 13620 } ], "hgvs": [ "NG_008072.1:g.13621G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000817" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 625, "referenceAllele": "G", "start": 624 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.7:c.440G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly147Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly147Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS747643" }, { "coordinates": [ { "allele": "A", "end": 802, "referenceAllele": "G", "start": 801 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.8:c.647G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly216Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly216Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS752395", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.647G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.647G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly216Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly216Asp" } } } }, { "coordinates": [ { "allele": "A", "end": 440, "referenceAllele": "G", "start": 439 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000337299.6:c.440G>A" ], "proteinEffect": { "hgvs": "ENSP00000338213.6:p.Gly147Asp", "hgvsWellDefined": "ENSP00000338213.6:p.Gly147Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS260445" }, { "coordinates": [ { "allele": "A", "end": 812, "referenceAllele": "G", "start": 811 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "ENST00000380518.7:c.647G>A" ], "proteinEffect": { "hgvs": "ENSP00000369889.3:p.Gly216Asp", "hgvsWellDefined": "ENSP00000369889.3:p.Gly216Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS272956" }, { "@id": "http://reg.genome.network/allele/PA645416294", "coordinates": [ { "allele": "A", "end": 828, "referenceAllele": "G", "start": 827 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.4:c.647G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly216Asp", "hgvsWellDefined": "NP_001835.3:p.Gly216Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS027172" }, { "@id": "http://reg.genome.network/allele/PA2830097098", "coordinates": [ { "allele": "A", "end": 621, "referenceAllele": "G", "start": 620 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.2:c.440G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly147Asp", "hgvsWellDefined": "NP_149162.2:p.Gly147Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS039568" }, { "coordinates": [ { "allele": "A", "end": 1380, "referenceAllele": "G", "start": 1379 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_006719242.2:c.791G>A" ], "proteinEffect": { "hgvs": "XP_006719305.2:p.Gly264Asp", "hgvsWellDefined": "XP_006719305.2:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS073018" }, { "coordinates": [ { "allele": "A", "end": 1557, "referenceAllele": "G", "start": 1556 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537928.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536230.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536230.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104886" }, { "coordinates": [ { "allele": "A", "end": 1148, "referenceAllele": "G", "start": 1147 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537929.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536231.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536231.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104887" }, { "coordinates": [ { "allele": "A", "end": 1149, "referenceAllele": "G", "start": 1148 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537930.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536232.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536232.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104888" }, { "coordinates": [ { "allele": "A", "end": 1131, "referenceAllele": "G", "start": 1130 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537931.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536233.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536233.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104889" }, { "coordinates": [ { "allele": "A", "end": 1475, "referenceAllele": "G", "start": 1474 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537932.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536234.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536234.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104890" }, { "coordinates": [ { "allele": "A", "end": 1109, "referenceAllele": "G", "start": 1108 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537933.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_011536235.1:p.Gly264Asp", "hgvsWellDefined": "XP_011536235.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104891" }, { "coordinates": [ { "allele": "A", "end": 1554, "referenceAllele": "G", "start": 1553 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_011537934.1:c.788G>A" ], "proteinEffect": { "hgvs": "XP_011536236.1:p.Gly263Asp", "hgvsWellDefined": "XP_011536236.1:p.Gly263Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS104892" }, { "coordinates": [ { "allele": "A", "end": 913, "referenceAllele": "G", "start": 912 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018828.1:c.791G>A" ], "proteinEffect": { "hgvs": "XP_016874317.1:p.Gly264Asp", "hgvsWellDefined": "XP_016874317.1:p.Gly264Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570670" }, { "coordinates": [ { "allele": "A", "end": 910, "referenceAllele": "G", "start": 909 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018829.1:c.788G>A" ], "proteinEffect": { "hgvs": "XP_016874318.1:p.Gly263Asp", "hgvsWellDefined": "XP_016874318.1:p.Gly263Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570671" }, { "coordinates": [ { "allele": "A", "end": 703, "referenceAllele": "G", "start": 702 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018830.1:c.581G>A" ], "proteinEffect": { "hgvs": "XP_016874319.1:p.Gly194Asp", "hgvsWellDefined": "XP_016874319.1:p.Gly194Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570672" }, { "coordinates": [ { "allele": "A", "end": 1136, "referenceAllele": "G", "start": 1135 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "XM_017018831.2:c.101G>A" ], "proteinEffect": { "hgvs": "XP_016874320.1:p.Gly34Asp", "hgvsWellDefined": "XP_016874320.1:p.Gly34Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS570673" }, { "@id": "http://reg.genome.network/allele/PA645416294", "coordinates": [ { "allele": "A", "end": 802, "referenceAllele": "G", "start": 801 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_001844.5:c.647G>A" ], "proteinEffect": { "hgvs": "NP_001835.3:p.Gly216Asp", "hgvsWellDefined": "NP_001835.3:p.Gly216Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS665206", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000380518.8:c.647G>A" }, "RefSeq": { "hgvs": "NM_001844.5:c.647G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000369889.3:p.Gly216Asp" }, "RefSeq": { "hgvs": "NP_001835.3:p.Gly216Asp" } } } }, { "@id": "http://reg.genome.network/allele/PA2830097098", "coordinates": [ { "allele": "A", "end": 595, "referenceAllele": "G", "start": 594 } ], "gene": "http://reg.genome.network/gene/GN002200", "geneNCBI_id": 1280, "geneSymbol": "COL2A1", "hgvs": [ "NM_033150.3:c.440G>A" ], "proteinEffect": { "hgvs": "NP_149162.2:p.Gly147Asp", "hgvsWellDefined": "NP_149162.2:p.Gly147Asp" }, "referenceSequence": "http://reg.genome.network/refseq/RS699283" } ], "type": "nucleotide" }