{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA338422026", "communityStandardTitle": [ "NM_005957.5(MTHFR):c.523G>A (p.Ala175Thr)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1490468[alleleid]", "alleleId": 1490468, "preferredName": "NM_005957.5(MTHFR):c.523G>A (p.Ala175Thr)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/1445597", "RCV": [ "RCV001985134", "RCV003471099" ], "variationId": 1445597 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.11860332C>T?assembly=hg19", "id": "chr1:g.11860332C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.11800275C>T?assembly=hg38", "id": "chr1:g.11800275C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1182635980", "rs": 1182635980 } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-11800275-C-T?dataset=gnomad_r4", "id": "1-11800275-C-T", "variant": "1:11800275 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 11800275, "referenceAllele": "C", "start": 11800274 } ], "hgvs": [ "NC_000001.11:g.11800275C>T", "CM000663.2:g.11800275C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 11860332, "referenceAllele": "C", "start": 11860331 } ], "hgvs": [ "NC_000001.10:g.11860332C>T", "CM000663.1:g.11860332C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 11782919, "referenceAllele": "C", "start": 11782918 } ], "hgvs": [ "NC_000001.9:g.11782919C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 10829, "referenceAllele": "G", "start": 10828 } ], "hgvs": [ "NG_013351.1:g.10829G>A", "LRG_726:g.10829G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS002803" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 709, "referenceAllele": "G", "start": 708 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376486.3:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000365669.3:p.Ala175Thr", "hgvsWellDefined": "ENSP00000365669.3:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS751771" }, { "coordinates": [ { "allele": "A", "end": 1698, "referenceAllele": "G", "start": 1697 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376585.6:c.646G>A" ], "proteinEffect": { "hgvs": "ENSP00000365770.1:p.Ala216Thr", "hgvsWellDefined": "ENSP00000365770.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS751786" }, { "coordinates": [ { "allele": "A", "end": 613, "referenceAllele": "G", "start": 612 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376590.9:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000365775.3:p.Ala175Thr", "hgvsWellDefined": "ENSP00000365775.3:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS751788", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000376590.9:c.523G>A" }, "RefSeq": { "hgvs": "NM_005957.5:c.523G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000365775.3:p.Ala175Thr" }, "RefSeq": { "hgvs": "NP_005948.3:p.Ala175Thr" } } } }, { "coordinates": [ { "allele": "A", "end": 1973, "referenceAllele": "G", "start": 1972 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376592.6:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000365777.1:p.Ala175Thr", "hgvsWellDefined": "ENSP00000365777.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS751789" }, { "coordinates": [ { "allele": "A", "end": 655, "referenceAllele": "G", "start": 654 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000423400.7:c.643G>A" ], "proteinEffect": { "hgvs": "ENSP00000398908.3:p.Ala215Thr", "hgvsWellDefined": "ENSP00000398908.3:p.Ala215Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS754979" }, { "coordinates": [ { "allele": "A", "end": 790, "referenceAllele": "G", "start": 789 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641407.1:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000493098.1:p.Ala175Thr", "hgvsWellDefined": "ENSP00000493098.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS766063" }, { "coordinates": [ { "allele": "A", "end": 1493, "referenceAllele": "G", "start": 1492 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641437.1:n.1493G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS766082" }, { "coordinates": [ { "allele": "A", "end": 651, "referenceAllele": "G", "start": 650 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641446.1:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000493262.1:p.Ala175Thr", "hgvsWellDefined": "ENSP00000493262.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS766088" }, { "coordinates": [ { "allele": "A", "end": 580, "referenceAllele": "G", "start": 579 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641721.1:n.580G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS766290" }, { "coordinates": [ { "allele": "A", "end": 865, "referenceAllele": "G", "start": 864 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641747.1:c.*35G>A" ], "proteinEffect": { "hgvs": "ENSP00000493116.1:n.*35G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS766307" }, { "coordinates": [ { "allele": "A", "end": 658, "referenceAllele": "G", "start": 657 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641759.1:n.658G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS766315" }, { "coordinates": [ { "allele": "A", "end": 806, "referenceAllele": "G", "start": 805 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641805.1:n.806G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS766348" }, { "coordinates": [ { "allele": "A", "end": 1771, "referenceAllele": "G", "start": 1770 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641909.1:n.1771G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS766428" }, { "coordinates": [ { "allele": "A", "end": 646, "referenceAllele": "G", "start": 645 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376583.7:c.646G>A" ], "proteinEffect": { "hgvs": "ENSP00000365767.3:p.Ala216Thr", "hgvsWellDefined": "ENSP00000365767.3:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS271231" }, { "coordinates": [ { "allele": "A", "end": 1698, "referenceAllele": "G", "start": 1697 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376585.5:c.646G>A" ], "proteinEffect": { "hgvs": "ENSP00000365770.1:p.Ala216Thr", "hgvsWellDefined": "ENSP00000365770.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS271232" }, { "coordinates": [ { "allele": "A", "end": 707, "referenceAllele": "G", "start": 706 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376590.7:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000365775.3:p.Ala175Thr", "hgvsWellDefined": "ENSP00000365775.3:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS271234" }, { "coordinates": [ { "allele": "A", "end": 652, "referenceAllele": "G", "start": 651 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376592.5:c.523G>A" ], "proteinEffect": { "hgvs": "ENSP00000365777.1:p.Ala175Thr", "hgvsWellDefined": "ENSP00000365777.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS271235" }, { "@id": "http://reg.genome.network/allele/PA2579899187", "coordinates": [ { "allele": "A", "end": 752, "referenceAllele": "G", "start": 751 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_005957.4:c.523G>A", "LRG_726t1:c.523G>A" ], "proteinEffect": { "hgvs": "NP_005948.3:p.Ala175Thr", "hgvsWellDefined": "NP_005948.3:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS031008" }, { "coordinates": [ { "allele": "A", "end": 1589, "referenceAllele": "G", "start": 1588 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263458.2:c.646G>A" ], "proteinEffect": { "hgvs": "XP_005263515.1:p.Ala216Thr", "hgvsWellDefined": "XP_005263515.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS063811" }, { "coordinates": [ { "allele": "A", "end": 1194, "referenceAllele": "G", "start": 1193 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263460.3:c.523G>A" ], "proteinEffect": { "hgvs": "XP_005263517.1:p.Ala175Thr", "hgvsWellDefined": "XP_005263517.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS063812" }, { "coordinates": [ { "allele": "A", "end": 1062, "referenceAllele": "G", "start": 1061 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263461.3:c.523G>A" ], "proteinEffect": { "hgvs": "XP_005263518.1:p.Ala175Thr", "hgvsWellDefined": "XP_005263518.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS063813" }, { "coordinates": [ { "allele": "A", "end": 650, "referenceAllele": "G", "start": 649 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263462.3:c.523G>A" ], "proteinEffect": { "hgvs": "XP_005263519.1:p.Ala175Thr", "hgvsWellDefined": "XP_005263519.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS063814" }, { "coordinates": [ { "allele": "A", "end": 769, "referenceAllele": "G", "start": 768 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263463.2:c.277G>A" ], "proteinEffect": { "hgvs": "XP_005263520.1:p.Ala93Thr", "hgvsWellDefined": "XP_005263520.1:p.Ala93Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS063815" }, { "coordinates": [ { "allele": "A", "end": 1586, "referenceAllele": "G", "start": 1585 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541495.1:c.643G>A" ], "proteinEffect": { "hgvs": "XP_011539797.1:p.Ala215Thr", "hgvsWellDefined": "XP_011539797.1:p.Ala215Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108432" }, { "coordinates": [ { "allele": "A", "end": 1589, "referenceAllele": "G", "start": 1588 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541496.1:c.646G>A" ], "proteinEffect": { "hgvs": "XP_011539798.1:p.Ala216Thr", "hgvsWellDefined": "XP_011539798.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108433" }, { "@id": "http://reg.genome.network/allele/PA2573202133", "coordinates": [ { "allele": "A", "end": 809, "referenceAllele": "G", "start": 808 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_001330358.1:c.646G>A" ], "proteinEffect": { "hgvs": "NP_001317287.1:p.Ala216Thr", "hgvsWellDefined": "NP_001317287.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS516743" }, { "coordinates": [ { "allele": "A", "end": 1139, "referenceAllele": "G", "start": 1138 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263460.5:c.523G>A" ], "proteinEffect": { "hgvs": "XP_005263517.1:p.Ala175Thr", "hgvsWellDefined": "XP_005263517.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS535677" }, { "coordinates": [ { "allele": "A", "end": 640, "referenceAllele": "G", "start": 639 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263462.4:c.523G>A" ], "proteinEffect": { "hgvs": "XP_005263519.1:p.Ala175Thr", "hgvsWellDefined": "XP_005263519.1:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS535678" }, { "coordinates": [ { "allele": "A", "end": 769, "referenceAllele": "G", "start": 768 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263463.4:c.277G>A" ], "proteinEffect": { "hgvs": "XP_005263520.1:p.Ala93Thr", "hgvsWellDefined": "XP_005263520.1:p.Ala93Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS535679" }, { "coordinates": [ { "allele": "A", "end": 1390, "referenceAllele": "G", "start": 1389 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541495.3:c.643G>A" ], "proteinEffect": { "hgvs": "XP_011539797.1:p.Ala215Thr", "hgvsWellDefined": "XP_011539797.1:p.Ala215Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS554458" }, { "coordinates": [ { "allele": "A", "end": 669, "referenceAllele": "G", "start": 668 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541496.3:c.646G>A" ], "proteinEffect": { "hgvs": "XP_011539798.1:p.Ala216Thr", "hgvsWellDefined": "XP_011539798.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS554459" }, { "coordinates": [ { "allele": "A", "end": 669, "referenceAllele": "G", "start": 668 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_017001328.2:c.646G>A" ], "proteinEffect": { "hgvs": "XP_016856817.1:p.Ala216Thr", "hgvsWellDefined": "XP_016856817.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557530" }, { "coordinates": [ { "allele": "A", "end": 675, "referenceAllele": "G", "start": 674 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_024447198.1:c.277G>A" ], "proteinEffect": { "hgvs": "XP_024302966.1:p.Ala93Thr", "hgvsWellDefined": "XP_024302966.1:p.Ala93Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS580792" }, { "coordinates": [ { "allele": "A", "end": 1390, "referenceAllele": "G", "start": 1389 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XR_002956640.1:n.1390G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS602779" }, { "@id": "http://reg.genome.network/allele/PA2579899187", "coordinates": [ { "allele": "A", "end": 613, "referenceAllele": "G", "start": 612 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_005957.5:c.523G>A" ], "proteinEffect": { "hgvs": "NP_005948.3:p.Ala175Thr", "hgvsWellDefined": "NP_005948.3:p.Ala175Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS696571", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000376590.9:c.523G>A" }, "RefSeq": { "hgvs": "NM_005957.5:c.523G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000365775.3:p.Ala175Thr" }, "RefSeq": { "hgvs": "NP_005948.3:p.Ala175Thr" } } } }, { "@id": "http://reg.genome.network/allele/PA2573202133", "coordinates": [ { "allele": "A", "end": 669, "referenceAllele": "G", "start": 668 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_001330358.2:c.646G>A" ], "proteinEffect": { "hgvs": "NP_001317287.1:p.Ala216Thr", "hgvsWellDefined": "NP_001317287.1:p.Ala216Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS718659" } ], "type": "nucleotide" }