{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA351595240", "communityStandardTitle": [ "NM_005677.4(COLQ):c.1318T>C (p.Cys440Arg)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1925539[alleleid]", "alleleId": 1925539, "preferredName": "NM_005677.4(COLQ):c.1318T>C (p.Cys440Arg)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2203310", "RCV": [ "RCV002651642" ], "variationId": 2203310 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.15493201A>G?assembly=hg19", "id": "chr3:g.15493201A>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr3:g.15451694A>G?assembly=hg38", "id": "chr3:g.15451694A>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1559510028", "rs": 1559510028 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/3-15451694-A-G?dataset=gnomad_r4", "id": "3-15451694-A-G", "variant": "3:15451694 A / G" } ] }, "genomicAlleles": [ { "chromosome": "3", "coordinates": [ { "allele": "G", "end": 15451694, "referenceAllele": "A", "start": 15451693 } ], "hgvs": [ "NC_000003.12:g.15451694A>G", "CM000665.2:g.15451694A>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000051" }, { "chromosome": "3", "coordinates": [ { "allele": "G", "end": 15493201, "referenceAllele": "A", "start": 15493200 } ], "hgvs": [ "NC_000003.11:g.15493201A>G", "CM000665.1:g.15493201A>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000027" }, { "chromosome": "3", "coordinates": [ { "allele": "G", "end": 15468205, "referenceAllele": "A", "start": 15468204 } ], "hgvs": [ "NC_000003.10:g.15468205A>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000003" }, { "coordinates": [ { "allele": "C", "end": 75058, "referenceAllele": "T", "start": 75057 } ], "hgvs": [ "NG_009032.1:g.75058T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS001392" }, { "coordinates": [ { "allele": "C", "end": 75058, "referenceAllele": "T", "start": 75057 } ], "hgvs": [ "NG_009032.2:g.75058T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS673516" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "C", "end": 149, "referenceAllele": "T", "start": 148 } ], "gene": "http://reg.genome.network/gene/GN042328", "geneNCBI_id": 100873956, "geneSymbol": "EAF1-AS1", "hgvs": [ "ENST00000608408.2:n.149T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS914355" }, { "coordinates": [ { "allele": "C", "end": 165, "referenceAllele": "T", "start": 164 } ], "hgvs": [ "ENST00000629729.3:c.165T>C" ], "proteinEffect": { "hgvs": "ENSP00000518887.1:n.165T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS914378" }, { "coordinates": [ { "allele": "C", "end": 1399, "referenceAllele": "T", "start": 1398 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000383788.10:c.1318T>C" ], "proteinEffect": { "hgvs": "ENSP00000373298.3:p.Cys440Arg", "hgvsWellDefined": "ENSP00000373298.3:p.Cys440Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS752731", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000383788.10:c.1318T>C" }, "RefSeq": { "hgvs": "NM_005677.4:c.1318T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000373298.3:p.Cys440Arg" }, "RefSeq": { "hgvs": "NP_005668.2:p.Cys440Arg" } } } }, { "coordinates": [ { "allele": "C", "end": 1174, "referenceAllele": "T", "start": 1173 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000604401.2:n.1174T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS761610" }, { "coordinates": [ { "allele": "C", "end": 1400, "referenceAllele": "T", "start": 1399 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000679838.1:c.*1080T>C" ], "proteinEffect": { "hgvs": "ENSP00000505708.1:n.*1080T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS779460" }, { "coordinates": [ { "allele": "C", "end": 1230, "referenceAllele": "T", "start": 1229 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000680240.1:n.1230T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS779860" }, { "coordinates": [ { "allele": "C", "end": 1084, "referenceAllele": "T", "start": 1083 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000680545.1:n.1084T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS780161" }, { "coordinates": [ { "allele": "C", "end": 783, "referenceAllele": "T", "start": 782 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000680897.1:n.783T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS780511" }, { "coordinates": [ { "allele": "C", "end": 1269, "referenceAllele": "T", "start": 1268 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000681097.1:c.*332T>C" ], "proteinEffect": { "hgvs": "ENSP00000505397.1:n.*332T>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS780709" }, { "coordinates": [ { "allele": "C", "end": 4809, "referenceAllele": "T", "start": 4808 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000681222.1:n.4809T>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS780833" }, { "coordinates": [ { "allele": "C", "end": 1573, "referenceAllele": "T", "start": 1572 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000383781.8:c.1288T>C" ], "proteinEffect": { "hgvs": "ENSP00000373291.3:p.Cys430Arg", "hgvsWellDefined": "ENSP00000373291.3:p.Cys430Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS274030" }, { "coordinates": [ { "allele": "C", "end": 1327, "referenceAllele": "T", "start": 1326 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000383786.9:c.1216T>C" ], "proteinEffect": { "hgvs": "ENSP00000373296.3:p.Cys406Arg", "hgvsWellDefined": "ENSP00000373296.3:p.Cys406Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS274031" }, { "coordinates": [ { "allele": "C", "end": 1444, "referenceAllele": "T", "start": 1443 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000383788.9:c.1318T>C" ], "proteinEffect": { "hgvs": "ENSP00000373298.3:p.Cys440Arg", "hgvsWellDefined": "ENSP00000373298.3:p.Cys440Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS274032" }, { "coordinates": [ { "allele": "C", "end": 1447, "referenceAllele": "T", "start": 1446 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "ENST00000603808.5:c.1321T>C" ], "proteinEffect": { "hgvs": "ENSP00000474271.1:p.Cys441Arg", "hgvsWellDefined": "ENSP00000474271.1:p.Cys441Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS398772" }, { "@id": "http://reg.genome.network/allele/PA2580318195", "coordinates": [ { "allele": "C", "end": 1444, "referenceAllele": "T", "start": 1443 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "NM_005677.3:c.1318T>C" ], "proteinEffect": { "hgvs": "NP_005668.2:p.Cys440Arg", "hgvsWellDefined": "NP_005668.2:p.Cys440Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS030761" }, { "@id": "http://reg.genome.network/allele/PA2830156751", "coordinates": [ { "allele": "C", "end": 1573, "referenceAllele": "T", "start": 1572 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "NM_080538.2:c.1288T>C" ], "proteinEffect": { "hgvs": "NP_536799.1:p.Cys430Arg", "hgvsWellDefined": "NP_536799.1:p.Cys430Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS040165" }, { "@id": "http://reg.genome.network/allele/PA2830156965", "coordinates": [ { "allele": "C", "end": 1342, "referenceAllele": "T", "start": 1341 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "NM_080539.3:c.1216T>C" ], "proteinEffect": { "hgvs": "NP_536800.2:p.Cys406Arg", "hgvsWellDefined": "NP_536800.2:p.Cys406Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS040166" }, { "@id": "http://reg.genome.network/allele/PA2580318195", "coordinates": [ { "allele": "C", "end": 1399, "referenceAllele": "T", "start": 1398 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "NM_005677.4:c.1318T>C" ], "proteinEffect": { "hgvs": "NP_005668.2:p.Cys440Arg", "hgvsWellDefined": "NP_005668.2:p.Cys440Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS667090", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000383788.10:c.1318T>C" }, "RefSeq": { "hgvs": "NM_005677.4:c.1318T>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000373298.3:p.Cys440Arg" }, "RefSeq": { "hgvs": "NP_005668.2:p.Cys440Arg" } } } }, { "@id": "http://reg.genome.network/allele/PA2830156965", "coordinates": [ { "allele": "C", "end": 1297, "referenceAllele": "T", "start": 1296 } ], "gene": "http://reg.genome.network/gene/GN002226", "geneNCBI_id": 8292, "geneSymbol": "COLQ", "hgvs": [ "NM_080539.4:c.1216T>C" ], "proteinEffect": { "hgvs": "NP_536800.2:p.Cys406Arg", "hgvsWellDefined": "NP_536800.2:p.Cys406Arg" }, "referenceSequence": "http://reg.genome.network/refseq/RS699512" } ], "type": "nucleotide" }