{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA1636791", "communityStandardTitle": [ "NM_022436.3(ABCG5):c.139G>T (p.Val47Phe)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=884933[alleleid]", "alleleId": 884933, "preferredName": "NM_022436.3(ABCG5):c.139G>T (p.Val47Phe)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/895028", "RCV": [ "RCV001136896", "RCV001512079", "RCV002468177", "RCV002261289", "RCV003293896", "RCV003331050", "RCV003938487" ], "variationId": 895028 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-44065680-C-A", "id": "2-44065680-C-A", "variant": "2:44065680 C / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.44065680C>A?assembly=hg19", "id": "chr2:g.44065680C>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.43838541C>A?assembly=hg38", "id": "chr2:g.43838541C>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/72542426", "rs": 72542426 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-44065680-C-A?dataset=gnomad_r2_1", "id": "2-44065680-C-A", "variant": "2:44065680 C / A" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-43838541-C-A?dataset=gnomad_r3", "id": "2-43838541-C-A", "variant": "2:43838541 C / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-43838541-C-A?dataset=gnomad_r4", "id": "2-43838541-C-A", "variant": "2:43838541 C / A" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 43838541, "referenceAllele": "C", "start": 43838540 } ], "hgvs": [ "NC_000002.12:g.43838541C>A", "CM000664.2:g.43838541C>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 44065680, "referenceAllele": "C", "start": 44065679 } ], "hgvs": [ "NC_000002.11:g.44065680C>A", "CM000664.1:g.44065680C>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 43919184, "referenceAllele": "C", "start": 43919183 } ], "hgvs": [ "NC_000002.10:g.43919184C>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "T", "end": 5279, "referenceAllele": "G", "start": 5278 } ], "hgvs": [ "NG_008883.1:g.5279G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS001278" }, { "coordinates": [ { "allele": "A", "end": 4578, "referenceAllele": "C", "start": 4577 } ], "hgvs": [ "NG_008884.1:g.4578C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001279" }, { "coordinates": [ { "allele": "A", "end": 11600, "referenceAllele": "C", "start": 11599 } ], "hgvs": [ "NG_008884.2:g.11600C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS706090" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 299, "referenceAllele": "G", "start": 298 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000405322.8:c.139G>T" ], "proteinEffect": { "hgvs": "ENSP00000384513.2:p.Val47Phe", "hgvsWellDefined": "ENSP00000384513.2:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS754122", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000405322.8:c.139G>T" }, "RefSeq": { "hgvs": "NM_022436.3:c.139G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000384513.2:p.Val47Phe" }, "RefSeq": { "hgvs": "NP_071881.1:p.Val47Phe" } } } }, { "coordinates": [ { "allele": "A", "end": 520, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 520, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "ENST00000643284.1:n.520+5880C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS767195" }, { "coordinates": [ { "allele": "A", "end": 720, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 720, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "ENST00000644611.1:c.75+5880C>A" ], "proteinEffect": { "hgvs": "ENSP00000495423.1:n.75+5880C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS767900" }, { "coordinates": [ { "allele": "T", "end": 212, "referenceAllele": "G", "start": 211 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000644754.1:n.212G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS767979" }, { "coordinates": [ { "allele": "T", "end": 279, "referenceAllele": "G", "start": 278 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000260645.5:c.139G>T" ], "proteinEffect": { "hgvs": "ENSP00000260645.1:p.Val47Phe", "hgvsWellDefined": "ENSP00000260645.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS250618" }, { "coordinates": [ { "allele": "T", "end": 212, "referenceAllele": "G", "start": 211 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000405322.5:c.-686G>T" ], "proteinEffect": { "hgvs": "ENSP00000384513.1:n.-686G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS280311" }, { "coordinates": [ { "allele": "T", "end": 325, "referenceAllele": "G", "start": 324 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000409962.1:c.-686G>T" ], "proteinEffect": { "hgvs": "ENSP00000386501.1:n.-686G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS282000" }, { "coordinates": [ { "allele": "T", "end": 210, "referenceAllele": "G", "start": 209 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "ENST00000486512.5:c.-686G>T" ], "proteinEffect": { "hgvs": "ENSP00000430935.1:n.-686G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS325308" }, { "@id": "http://reg.genome.network/allele/PA1139749868", "coordinates": [ { "allele": "T", "end": 279, "referenceAllele": "G", "start": 278 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "NM_022436.2:c.139G>T" ], "proteinEffect": { "hgvs": "NP_071881.1:p.Val47Phe", "hgvsWellDefined": "NP_071881.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS037306" }, { "coordinates": [ { "allele": "T", "end": 279, "referenceAllele": "G", "start": 278 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_005264480.2:c.139G>T" ], "proteinEffect": { "hgvs": "XP_005264537.1:p.Val47Phe", "hgvsWellDefined": "XP_005264537.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS064250" }, { "coordinates": [ { "allele": "T", "end": 277, "referenceAllele": "G", "start": 276 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_006712073.2:c.139G>T" ], "proteinEffect": { "hgvs": "XP_006712136.1:p.Val47Phe", "hgvsWellDefined": "XP_006712136.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS069455" }, { "coordinates": [ { "allele": "T", "end": 297, "referenceAllele": "G", "start": 296 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_006712074.2:c.139G>T" ], "proteinEffect": { "hgvs": "XP_006712137.1:p.Val47Phe", "hgvsWellDefined": "XP_006712137.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS069456" }, { "coordinates": [ { "allele": "T", "end": 275, "referenceAllele": "G", "start": 274 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533024.1:c.139G>T" ], "proteinEffect": { "hgvs": "XP_011531326.1:p.Val47Phe", "hgvsWellDefined": "XP_011531326.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS100050" }, { "coordinates": [ { "allele": "T", "end": 325, "referenceAllele": "G", "start": 324 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533025.1:c.-605G>T" ], "proteinEffect": { "hgvs": "XP_011531327.1:n.-605G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS100051" }, { "coordinates": [ { "allele": "T", "end": 276, "referenceAllele": "G", "start": 275 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533026.1:c.139G>T" ], "proteinEffect": { "hgvs": "XP_011531328.1:p.Val47Phe", "hgvsWellDefined": "XP_011531328.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS100052" }, { "coordinates": [ { "allele": "T", "end": 325, "referenceAllele": "G", "start": 324 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533027.1:c.-720G>T" ], "proteinEffect": { "hgvs": "XP_011531329.1:n.-720G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS100053" }, { "coordinates": [ { "allele": "A", "end": 565, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 565, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XM_011533029.1:c.75+5880C>A" ], "proteinEffect": { "hgvs": "XP_011531331.1:n.75+5880C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS100055" }, { "coordinates": [ { "allele": "A", "end": 566, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 566, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XM_011533030.1:c.75+5880C>A" ], "proteinEffect": { "hgvs": "XP_011531332.1:n.75+5880C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS100056" }, { "coordinates": [ { "allele": "A", "end": 1843, "endIntronDirection": "-", "endIntronOffset": 5965, "referenceAllele": "C", "start": 1843, "startIntronDirection": "-", "startIntronOffset": 5966 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XM_011533031.1:c.-153-5966C>A" ], "proteinEffect": { "hgvs": "XP_011531333.1:n.-153-5966C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS100057" }, { "coordinates": [ { "allele": "A", "end": 565, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 565, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XR_939707.1:n.565+5880C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS134403" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_005264480.4:c.139G>T" ], "proteinEffect": { "hgvs": "XP_005264537.1:p.Val47Phe", "hgvsWellDefined": "XP_005264537.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS535887" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_006712073.3:c.139G>T" ], "proteinEffect": { "hgvs": "XP_006712136.1:p.Val47Phe", "hgvsWellDefined": "XP_006712136.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS538166" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_006712074.3:c.139G>T" ], "proteinEffect": { "hgvs": "XP_006712137.1:p.Val47Phe", "hgvsWellDefined": "XP_006712137.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS538167" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533024.2:c.139G>T" ], "proteinEffect": { "hgvs": "XP_011531326.1:p.Val47Phe", "hgvsWellDefined": "XP_011531326.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS551078" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533025.3:c.-605G>T" ], "proteinEffect": { "hgvs": "XP_011531327.1:n.-605G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS551079" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533026.2:c.139G>T" ], "proteinEffect": { "hgvs": "XP_011531328.1:p.Val47Phe", "hgvsWellDefined": "XP_011531328.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS551080" }, { "coordinates": [ { "allele": "T", "end": 300, "referenceAllele": "G", "start": 299 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "XM_011533027.3:c.-720G>T" ], "proteinEffect": { "hgvs": "XP_011531329.1:n.-720G>T" }, "referenceSequence": "http://reg.genome.network/refseq/RS551081" }, { "coordinates": [ { "allele": "A", "end": 720, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 720, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XM_011533029.2:c.75+5880C>A" ], "proteinEffect": { "hgvs": "XP_011531331.1:n.75+5880C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS551083" }, { "coordinates": [ { "allele": "A", "end": 565, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 565, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XM_011533030.2:c.75+5880C>A" ], "proteinEffect": { "hgvs": "XP_011531332.1:n.75+5880C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS551084" }, { "coordinates": [ { "allele": "A", "end": 579, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 579, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XR_001738891.1:n.579+5880C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS589327" }, { "coordinates": [ { "allele": "A", "end": 579, "endIntronDirection": "+", "endIntronOffset": 5880, "referenceAllele": "C", "start": 579, "startIntronDirection": "+", "startIntronOffset": 5879 } ], "gene": "http://reg.genome.network/gene/GN013887", "geneNCBI_id": 64241, "geneSymbol": "ABCG8", "hgvs": [ "XR_939707.2:n.579+5880C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS612370" }, { "@id": "http://reg.genome.network/allele/PA1139749868", "coordinates": [ { "allele": "T", "end": 299, "referenceAllele": "G", "start": 298 } ], "gene": "http://reg.genome.network/gene/GN013886", "geneNCBI_id": 64240, "geneSymbol": "ABCG5", "hgvs": [ "NM_022436.3:c.139G>T" ], "proteinEffect": { "hgvs": "NP_071881.1:p.Val47Phe", "hgvsWellDefined": "NP_071881.1:p.Val47Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS698537", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000405322.8:c.139G>T" }, "RefSeq": { "hgvs": "NM_022436.3:c.139G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000384513.2:p.Val47Phe" }, "RefSeq": { "hgvs": "NP_071881.1:p.Val47Phe" } } } } ], "type": "nucleotide" }