{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA198583", "communityStandardTitle": [ "NM_005957.5(MTHFR):c.440A>C (p.Gln147Pro)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=185788[alleleid]", "alleleId": 185788, "preferredName": "NM_005957.5(MTHFR):c.440A>C (p.Gln147Pro)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/187875", "RCV": [ "RCV000167595" ], "variationId": 187875 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.11861253T>G?assembly=hg19", "id": "chr1:g.11861253T>G" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.11801196T>G?assembly=hg38", "id": "chr1:g.11801196T>G" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/786204013", "rs": 786204013 } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 11801196, "referenceAllele": "T", "start": 11801195 } ], "hgvs": [ "NC_000001.11:g.11801196T>G", "CM000663.2:g.11801196T>G" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 11861253, "referenceAllele": "T", "start": 11861252 } ], "hgvs": [ "NC_000001.10:g.11861253T>G", "CM000663.1:g.11861253T>G" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "G", "end": 11783840, "referenceAllele": "T", "start": 11783839 } ], "hgvs": [ "NC_000001.9:g.11783840T>G" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "G", "end": 47, "referenceAllele": "T", "start": 46 } ], "hgvs": [ "NG_008766.1:g.47T>G" ], "referenceSequence": "http://reg.genome.network/refseq/RS001205" }, { "coordinates": [ { "allele": "C", "end": 9908, "referenceAllele": "A", "start": 9907 } ], "hgvs": [ "NG_013351.1:g.9908A>C", "LRG_726:g.9908A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS002803" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "C", "end": 626, "referenceAllele": "A", "start": 625 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376486.3:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000365669.3:p.Gln147Pro", "hgvsWellDefined": "ENSP00000365669.3:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS751771" }, { "coordinates": [ { "allele": "C", "end": 1615, "referenceAllele": "A", "start": 1614 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376585.6:c.563A>C" ], "proteinEffect": { "hgvs": "ENSP00000365770.1:p.Gln188Pro", "hgvsWellDefined": "ENSP00000365770.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS751786" }, { "coordinates": [ { "allele": "C", "end": 530, "referenceAllele": "A", "start": 529 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376590.9:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000365775.3:p.Gln147Pro", "hgvsWellDefined": "ENSP00000365775.3:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS751788", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000376590.9:c.440A>C" }, "RefSeq": { "hgvs": "NM_005957.5:c.440A>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000365775.3:p.Gln147Pro" }, "RefSeq": { "hgvs": "NP_005948.3:p.Gln147Pro" } } } }, { "coordinates": [ { "allele": "C", "end": 1890, "referenceAllele": "A", "start": 1889 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376592.6:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000365777.1:p.Gln147Pro", "hgvsWellDefined": "ENSP00000365777.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS751789" }, { "coordinates": [ { "allele": "C", "end": 572, "referenceAllele": "A", "start": 571 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000423400.7:c.560A>C" ], "proteinEffect": { "hgvs": "ENSP00000398908.3:p.Gln187Pro", "hgvsWellDefined": "ENSP00000398908.3:p.Gln187Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS754979" }, { "coordinates": [ { "allele": "C", "end": 707, "referenceAllele": "A", "start": 706 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641407.1:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000493098.1:p.Gln147Pro", "hgvsWellDefined": "ENSP00000493098.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS766063" }, { "coordinates": [ { "allele": "C", "end": 572, "referenceAllele": "A", "start": 571 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641437.1:n.572A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS766082" }, { "coordinates": [ { "allele": "C", "end": 568, "referenceAllele": "A", "start": 567 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641446.1:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000493262.1:p.Gln147Pro", "hgvsWellDefined": "ENSP00000493262.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS766088" }, { "coordinates": [ { "allele": "C", "end": 497, "referenceAllele": "A", "start": 496 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641721.1:n.497A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS766290" }, { "coordinates": [ { "allele": "C", "end": 817, "endIntronDirection": "-", "endIntronOffset": 873, "referenceAllele": "A", "start": 817, "startIntronDirection": "-", "startIntronOffset": 874 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641747.1:c.237-874A>C" ], "proteinEffect": { "hgvs": "ENSP00000493116.1:n.237-874A>C" }, "referenceSequence": "http://reg.genome.network/refseq/RS766307" }, { "coordinates": [ { "allele": "C", "end": 575, "referenceAllele": "A", "start": 574 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641759.1:n.575A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS766315" }, { "coordinates": [ { "allele": "C", "end": 723, "referenceAllele": "A", "start": 722 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641805.1:n.723A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS766348" }, { "coordinates": [ { "allele": "C", "end": 850, "referenceAllele": "A", "start": 849 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000641909.1:n.850A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS766428" }, { "coordinates": [ { "allele": "C", "end": 563, "referenceAllele": "A", "start": 562 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376583.7:c.563A>C" ], "proteinEffect": { "hgvs": "ENSP00000365767.3:p.Gln188Pro", "hgvsWellDefined": "ENSP00000365767.3:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS271231" }, { "coordinates": [ { "allele": "C", "end": 1615, "referenceAllele": "A", "start": 1614 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376585.5:c.563A>C" ], "proteinEffect": { "hgvs": "ENSP00000365770.1:p.Gln188Pro", "hgvsWellDefined": "ENSP00000365770.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS271232" }, { "coordinates": [ { "allele": "C", "end": 624, "referenceAllele": "A", "start": 623 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376590.7:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000365775.3:p.Gln147Pro", "hgvsWellDefined": "ENSP00000365775.3:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS271234" }, { "coordinates": [ { "allele": "C", "end": 569, "referenceAllele": "A", "start": 568 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "ENST00000376592.5:c.440A>C" ], "proteinEffect": { "hgvs": "ENSP00000365777.1:p.Gln147Pro", "hgvsWellDefined": "ENSP00000365777.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS271235" }, { "@id": "http://reg.genome.network/allele/PA198585", "coordinates": [ { "allele": "C", "end": 669, "referenceAllele": "A", "start": 668 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_005957.4:c.440A>C", "LRG_726t1:c.440A>C" ], "proteinEffect": { "hgvs": "NP_005948.3:p.Gln147Pro", "hgvsWellDefined": "NP_005948.3:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS031008" }, { "coordinates": [ { "allele": "C", "end": 1506, "referenceAllele": "A", "start": 1505 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263458.2:c.563A>C" ], "proteinEffect": { "hgvs": "XP_005263515.1:p.Gln188Pro", "hgvsWellDefined": "XP_005263515.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS063811" }, { "coordinates": [ { "allele": "C", "end": 1111, "referenceAllele": "A", "start": 1110 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263460.3:c.440A>C" ], "proteinEffect": { "hgvs": "XP_005263517.1:p.Gln147Pro", "hgvsWellDefined": "XP_005263517.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS063812" }, { "coordinates": [ { "allele": "C", "end": 979, "referenceAllele": "A", "start": 978 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263461.3:c.440A>C" ], "proteinEffect": { "hgvs": "XP_005263518.1:p.Gln147Pro", "hgvsWellDefined": "XP_005263518.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS063813" }, { "coordinates": [ { "allele": "C", "end": 567, "referenceAllele": "A", "start": 566 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263462.3:c.440A>C" ], "proteinEffect": { "hgvs": "XP_005263519.1:p.Gln147Pro", "hgvsWellDefined": "XP_005263519.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS063814" }, { "coordinates": [ { "allele": "C", "end": 686, "referenceAllele": "A", "start": 685 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263463.2:c.194A>C" ], "proteinEffect": { "hgvs": "XP_005263520.1:p.Gln65Pro", "hgvsWellDefined": "XP_005263520.1:p.Gln65Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS063815" }, { "coordinates": [ { "allele": "C", "end": 1503, "referenceAllele": "A", "start": 1502 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541495.1:c.560A>C" ], "proteinEffect": { "hgvs": "XP_011539797.1:p.Gln187Pro", "hgvsWellDefined": "XP_011539797.1:p.Gln187Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS108432" }, { "coordinates": [ { "allele": "C", "end": 1506, "referenceAllele": "A", "start": 1505 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541496.1:c.563A>C" ], "proteinEffect": { "hgvs": "XP_011539798.1:p.Gln188Pro", "hgvsWellDefined": "XP_011539798.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS108433" }, { "@id": "http://reg.genome.network/allele/PA916027987", "coordinates": [ { "allele": "C", "end": 726, "referenceAllele": "A", "start": 725 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_001330358.1:c.563A>C" ], "proteinEffect": { "hgvs": "NP_001317287.1:p.Gln188Pro", "hgvsWellDefined": "NP_001317287.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS516743" }, { "coordinates": [ { "allele": "C", "end": 1056, "referenceAllele": "A", "start": 1055 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263460.5:c.440A>C" ], "proteinEffect": { "hgvs": "XP_005263517.1:p.Gln147Pro", "hgvsWellDefined": "XP_005263517.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS535677" }, { "coordinates": [ { "allele": "C", "end": 557, "referenceAllele": "A", "start": 556 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263462.4:c.440A>C" ], "proteinEffect": { "hgvs": "XP_005263519.1:p.Gln147Pro", "hgvsWellDefined": "XP_005263519.1:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS535678" }, { "coordinates": [ { "allele": "C", "end": 686, "referenceAllele": "A", "start": 685 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_005263463.4:c.194A>C" ], "proteinEffect": { "hgvs": "XP_005263520.1:p.Gln65Pro", "hgvsWellDefined": "XP_005263520.1:p.Gln65Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS535679" }, { "coordinates": [ { "allele": "C", "end": 1307, "referenceAllele": "A", "start": 1306 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541495.3:c.560A>C" ], "proteinEffect": { "hgvs": "XP_011539797.1:p.Gln187Pro", "hgvsWellDefined": "XP_011539797.1:p.Gln187Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS554458" }, { "coordinates": [ { "allele": "C", "end": 586, "referenceAllele": "A", "start": 585 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_011541496.3:c.563A>C" ], "proteinEffect": { "hgvs": "XP_011539798.1:p.Gln188Pro", "hgvsWellDefined": "XP_011539798.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS554459" }, { "coordinates": [ { "allele": "C", "end": 586, "referenceAllele": "A", "start": 585 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_017001328.2:c.563A>C" ], "proteinEffect": { "hgvs": "XP_016856817.1:p.Gln188Pro", "hgvsWellDefined": "XP_016856817.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS557530" }, { "coordinates": [ { "allele": "C", "end": 592, "referenceAllele": "A", "start": 591 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XM_024447198.1:c.194A>C" ], "proteinEffect": { "hgvs": "XP_024302966.1:p.Gln65Pro", "hgvsWellDefined": "XP_024302966.1:p.Gln65Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS580792" }, { "coordinates": [ { "allele": "C", "end": 1307, "referenceAllele": "A", "start": 1306 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "XR_002956640.1:n.1307A>C" ], "referenceSequence": "http://reg.genome.network/refseq/RS602779" }, { "@id": "http://reg.genome.network/allele/PA198585", "coordinates": [ { "allele": "C", "end": 530, "referenceAllele": "A", "start": 529 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_005957.5:c.440A>C" ], "proteinEffect": { "hgvs": "NP_005948.3:p.Gln147Pro", "hgvsWellDefined": "NP_005948.3:p.Gln147Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS696571", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000376590.9:c.440A>C" }, "RefSeq": { "hgvs": "NM_005957.5:c.440A>C" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000365775.3:p.Gln147Pro" }, "RefSeq": { "hgvs": "NP_005948.3:p.Gln147Pro" } } } }, { "@id": "http://reg.genome.network/allele/PA916027987", "coordinates": [ { "allele": "C", "end": 586, "referenceAllele": "A", "start": 585 } ], "gene": "http://reg.genome.network/gene/GN007436", "geneNCBI_id": 4524, "geneSymbol": "MTHFR", "hgvs": [ "NM_001330358.2:c.563A>C" ], "proteinEffect": { "hgvs": "NP_001317287.1:p.Gln188Pro", "hgvsWellDefined": "NP_001317287.1:p.Gln188Pro" }, "referenceSequence": "http://reg.genome.network/refseq/RS718659" } ], "type": "nucleotide" }