{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA201276", "communityStandardTitle": [ "NM_005529.7(HSPG2):c.2074G>A (p.Val692Met)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=191804[alleleid]", "alleleId": 191804, "preferredName": "NM_005529.7(HSPG2):c.2074G>A (p.Val692Met)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/194641", "RCV": [ "RCV000175061", "RCV000352369", "RCV000388323", "RCV000757384", "RCV002277349" ], "variationId": 194641 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-22206977-C-T", "id": "1-22206977-C-T", "variant": "1:22206977 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.22206977C>T?assembly=hg19", "id": "chr1:g.22206977C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.21880484C>T?assembly=hg38", "id": "chr1:g.21880484C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/143669458", "rs": 143669458 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-22206977-C-T?dataset=gnomad_r2_1", "id": "1-22206977-C-T", "variant": "1:22206977 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21880484-C-T?dataset=gnomad_r3", "id": "1-21880484-C-T", "variant": "1:21880484 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-21880484-C-T?dataset=gnomad_r4", "id": "1-21880484-C-T", "variant": "1:21880484 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 21880484, "referenceAllele": "C", "start": 21880483 } ], "hgvs": [ "NC_000001.11:g.21880484C>T", "CM000663.2:g.21880484C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22206977, "referenceAllele": "C", "start": 22206976 } ], "hgvs": [ "NC_000001.10:g.22206977C>T", "CM000663.1:g.22206977C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 22079564, "referenceAllele": "C", "start": 22079563 } ], "hgvs": [ "NC_000001.9:g.22079564C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 61774, "referenceAllele": "G", "start": 61773 } ], "hgvs": [ "NG_016740.1:g.61774G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS003265" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 2167, "referenceAllele": "G", "start": 2166 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.8:c.2074G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Val692Met", "hgvsWellDefined": "ENSP00000363827.3:p.Val692Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS751480", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.2074G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.2074G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Val692Met" }, "RefSeq": { "hgvs": "NP_005520.4:p.Val692Met" } } } }, { "coordinates": [ { "allele": "A", "end": 2154, "referenceAllele": "G", "start": 2153 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "ENST00000374695.7:c.2074G>A" ], "proteinEffect": { "hgvs": "ENSP00000363827.3:p.Val692Met", "hgvsWellDefined": "ENSP00000363827.3:p.Val692Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS270365" }, { "@id": "http://reg.genome.network/allele/PA916017904", "coordinates": [ { "allele": "A", "end": 2157, "referenceAllele": "G", "start": 2156 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.1:c.2077G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Val693Met", "hgvsWellDefined": "NP_001278789.1:p.Val693Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS024346" }, { "@id": "http://reg.genome.network/allele/PA201277", "coordinates": [ { "allele": "A", "end": 2154, "referenceAllele": "G", "start": 2153 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.6:c.2074G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Val692Met", "hgvsWellDefined": "NP_005520.4:p.Val692Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS030620" }, { "coordinates": [ { "allele": "A", "end": 2140, "referenceAllele": "G", "start": 2139 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710594.2:c.2125G>A" ], "proteinEffect": { "hgvs": "XP_006710657.1:p.Val709Met", "hgvsWellDefined": "XP_006710657.1:p.Val709Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS068699" }, { "coordinates": [ { "allele": "A", "end": 2092, "referenceAllele": "G", "start": 2091 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710595.2:c.2077G>A" ], "proteinEffect": { "hgvs": "XP_006710658.1:p.Val693Met", "hgvsWellDefined": "XP_006710658.1:p.Val693Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS068700" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710596.2:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_006710659.1:p.Val710Met", "hgvsWellDefined": "XP_006710659.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS068701" }, { "coordinates": [ { "allele": "A", "end": 2089, "referenceAllele": "G", "start": 2088 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_006710597.2:c.2074G>A" ], "proteinEffect": { "hgvs": "XP_006710660.1:p.Val692Met", "hgvsWellDefined": "XP_006710660.1:p.Val692Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS068702" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541317.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539619.1:p.Val710Met", "hgvsWellDefined": "XP_011539619.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108259" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Val710Met", "hgvsWellDefined": "XP_011539620.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108260" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541319.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539621.1:p.Val710Met", "hgvsWellDefined": "XP_011539621.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108261" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541320.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539622.1:p.Val710Met", "hgvsWellDefined": "XP_011539622.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108262" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541321.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539623.1:p.Val710Met", "hgvsWellDefined": "XP_011539623.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108263" }, { "coordinates": [ { "allele": "A", "end": 2151, "referenceAllele": "G", "start": 2150 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541322.1:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539624.1:p.Val710Met", "hgvsWellDefined": "XP_011539624.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS108264" }, { "coordinates": [ { "allele": "A", "end": 2143, "referenceAllele": "G", "start": 2142 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_011541318.2:c.2128G>A" ], "proteinEffect": { "hgvs": "XP_011539620.1:p.Val710Met", "hgvsWellDefined": "XP_011539620.1:p.Val710Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS554390" }, { "coordinates": [ { "allele": "A", "end": 2284, "referenceAllele": "G", "start": 2283 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001120.1:c.2269G>A" ], "proteinEffect": { "hgvs": "XP_016856609.1:p.Val757Met", "hgvsWellDefined": "XP_016856609.1:p.Val757Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS557347" }, { "coordinates": [ { "allele": "A", "end": 2233, "referenceAllele": "G", "start": 2232 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001121.1:c.2218G>A" ], "proteinEffect": { "hgvs": "XP_016856610.1:p.Val740Met", "hgvsWellDefined": "XP_016856610.1:p.Val740Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS557348" }, { "coordinates": [ { "allele": "A", "end": 2230, "referenceAllele": "G", "start": 2229 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "XM_017001122.1:c.2215G>A" ], "proteinEffect": { "hgvs": "XP_016856611.1:p.Val739Met", "hgvsWellDefined": "XP_016856611.1:p.Val739Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS557349" }, { "@id": "http://reg.genome.network/allele/PA201277", "coordinates": [ { "allele": "A", "end": 2167, "referenceAllele": "G", "start": 2166 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_005529.7:c.2074G>A" ], "proteinEffect": { "hgvs": "NP_005520.4:p.Val692Met", "hgvsWellDefined": "NP_005520.4:p.Val692Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS667014", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000374695.8:c.2074G>A" }, "RefSeq": { "hgvs": "NM_005529.7:c.2074G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000363827.3:p.Val692Met" }, "RefSeq": { "hgvs": "NP_005520.4:p.Val692Met" } } } }, { "@id": "http://reg.genome.network/allele/PA916017904", "coordinates": [ { "allele": "A", "end": 2170, "referenceAllele": "G", "start": 2169 } ], "gene": "http://reg.genome.network/gene/GN005273", "geneNCBI_id": 3339, "geneSymbol": "HSPG2", "hgvs": [ "NM_001291860.2:c.2077G>A" ], "proteinEffect": { "hgvs": "NP_001278789.1:p.Val693Met", "hgvsWellDefined": "NP_001278789.1:p.Val693Met" }, "referenceSequence": "http://reg.genome.network/refseq/RS682883" } ], "type": "nucleotide" }