{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA250651", "communityStandardTitle": [ "NM_000233.4(LHCGR):c.430G>T (p.Val144Phe)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=29450[alleleid]", "alleleId": 29450, "preferredName": "NM_000233.4(LHCGR):c.430G>T (p.Val144Phe)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/14411", "RCV": [ "RCV000015492" ], "variationId": 14411 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/2-48950789-C-A", "id": "2-48950789-C-A", "variant": "2:48950789 C / A" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.48950789C>A?assembly=hg19", "id": "chr2:g.48950789C>A" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr2:g.48723650C>A?assembly=hg38", "id": "chr2:g.48723650C>A" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/121912539", "rs": 121912539 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-48950789-C-A?dataset=gnomad_r2_1", "id": "2-48950789-C-A", "variant": "2:48950789 C / A" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/2-48723650-C-A?dataset=gnomad_r4", "id": "2-48723650-C-A", "variant": "2:48723650 C / A" } ] }, "genomicAlleles": [ { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 48723650, "referenceAllele": "C", "start": 48723649 } ], "hgvs": [ "NC_000002.12:g.48723650C>A", "CM000664.2:g.48723650C>A" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000050" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 48950789, "referenceAllele": "C", "start": 48950788 } ], "hgvs": [ "NC_000002.11:g.48950789C>A", "CM000664.1:g.48950789C>A" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000026" }, { "chromosome": "2", "coordinates": [ { "allele": "A", "end": 48804293, "referenceAllele": "C", "start": 48804292 } ], "hgvs": [ "NC_000002.10:g.48804293C>A" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000002" }, { "coordinates": [ { "allele": "T", "end": 37092, "referenceAllele": "G", "start": 37091 } ], "hgvs": [ "NG_008193.1:g.37092G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS000935" }, { "coordinates": [ { "allele": "A", "end": 198726, "referenceAllele": "C", "start": 198725 } ], "hgvs": [ "NG_033050.1:g.198726C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS005382" }, { "coordinates": [ { "allele": "T", "end": 37092, "referenceAllele": "G", "start": 37091 } ], "hgvs": [ "NG_008193.2:g.37092G>T" ], "referenceSequence": "http://reg.genome.network/refseq/RS673493" }, { "coordinates": [ { "allele": "A", "end": 198726, "referenceAllele": "C", "start": 198725 } ], "hgvs": [ "NG_033050.2:g.198726C>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS673879" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "T", "end": 483, "referenceAllele": "G", "start": 482 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000294954.12:c.430G>T" ], "proteinEffect": { "hgvs": "ENSP00000294954.6:p.Val144Phe", "hgvsWellDefined": "ENSP00000294954.6:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS744242", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000294954.12:c.430G>T" }, "RefSeq": { "hgvs": "NM_000233.4:c.430G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000294954.6:p.Val144Phe" }, "RefSeq": { "hgvs": "NP_000224.2:p.Val144Phe" } } } }, { "coordinates": [ { "allele": "T", "end": 452, "referenceAllele": "G", "start": 451 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000294954.11:c.430G>T" ], "proteinEffect": { "hgvs": "ENSP00000294954.6:p.Val144Phe", "hgvsWellDefined": "ENSP00000294954.6:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS254018" }, { "coordinates": [ { "allele": "T", "end": 489, "referenceAllele": "G", "start": 488 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000401907.5:c.430G>T" ], "proteinEffect": { "hgvs": "ENSP00000385406.1:p.Val144Phe", "hgvsWellDefined": "ENSP00000385406.1:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS279355" }, { "coordinates": [ { "allele": "A", "end": 3552, "endIntronDirection": "+", "endIntronOffset": 51970, "referenceAllele": "C", "start": 3552, "startIntronDirection": "+", "startIntronOffset": 51969 } ], "gene": "http://reg.genome.network/gene/GN030651", "geneNCBI_id": 286749, "geneSymbol": "STON1-GTF2A1L", "hgvs": [ "ENST00000402114.6:c.3441+51970C>A" ], "proteinEffect": { "hgvs": "ENSP00000385701.1:n.3441+51970C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS279412" }, { "coordinates": [ { "allele": "T", "end": 489, "referenceAllele": "G", "start": 488 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000403273.5:c.430G>T" ], "proteinEffect": { "hgvs": "ENSP00000385847.1:p.Val144Phe", "hgvsWellDefined": "ENSP00000385847.1:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS279759" }, { "coordinates": [ { "allele": "T", "end": 430, "referenceAllele": "G", "start": 429 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000405626.5:c.430G>T" ], "proteinEffect": { "hgvs": "ENSP00000386033.1:p.Val144Phe", "hgvsWellDefined": "ENSP00000386033.1:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS280400" }, { "coordinates": [ { "allele": "T", "end": 328, "referenceAllele": "G", "start": 327 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "ENST00000428232.2:c.328G>T" ], "proteinEffect": { "hgvs": "ENSP00000403748.1:p.Val110Phe", "hgvsWellDefined": "ENSP00000403748.1:p.Val110Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS290097" }, { "coordinates": [ { "allele": "A", "end": 276, "endIntronDirection": "-", "endIntronOffset": 9242, "referenceAllele": "C", "start": 276, "startIntronDirection": "-", "startIntronOffset": 9243 } ], "gene": "http://reg.genome.network/gene/GN030727", "geneNCBI_id": 11036, "geneSymbol": "GTF2A1L", "hgvs": [ "ENST00000508440.1:c.277-9243C>A" ], "proteinEffect": { "hgvs": "ENSP00000421474.1:n.277-9243C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS339460" }, { "coordinates": [ { "allele": "T", "end": 408, "referenceAllele": "G", "start": 407 } ], "hgvs": [ "ENST00000602369.3:c.355G>T" ], "proteinEffect": { "hgvs": "ENSP00000473498.1:p.Val119Phe", "hgvsWellDefined": "ENSP00000473498.1:p.Val119Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS398164" }, { "@id": "http://reg.genome.network/allele/PA113110", "coordinates": [ { "allele": "T", "end": 500, "referenceAllele": "G", "start": 499 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "NM_000233.3:c.430G>T" ], "proteinEffect": { "hgvs": "NP_000224.2:p.Val144Phe", "hgvsWellDefined": "NP_000224.2:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS006296" }, { "coordinates": [ { "allele": "A", "end": 3552, "endIntronDirection": "+", "endIntronOffset": 51970, "referenceAllele": "C", "start": 3552, "startIntronDirection": "+", "startIntronOffset": 51969 } ], "gene": "http://reg.genome.network/gene/GN030651", "geneNCBI_id": 286749, "geneSymbol": "STON1-GTF2A1L", "hgvs": [ "NM_001198593.1:c.3441+51970C>A" ], "proteinEffect": { "hgvs": "NP_001185522.1:n.3441+51970C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS016784" }, { "coordinates": [ { "allele": "T", "end": 408, "referenceAllele": "G", "start": 407 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "XM_011532828.1:c.355G>T" ], "proteinEffect": { "hgvs": "XP_011531130.1:p.Val119Phe", "hgvsWellDefined": "XP_011531130.1:p.Val119Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS099854" }, { "coordinates": [ { "allele": "T", "end": 408, "referenceAllele": "G", "start": 407 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "XM_011532829.1:c.355G>T" ], "proteinEffect": { "hgvs": "XP_011531131.1:p.Val119Phe", "hgvsWellDefined": "XP_011531131.1:p.Val119Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS099855" }, { "coordinates": [ { "allele": "T", "end": 408, "referenceAllele": "G", "start": 407 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "XM_011532830.1:c.355G>T" ], "proteinEffect": { "hgvs": "XP_011531132.1:p.Val119Phe", "hgvsWellDefined": "XP_011531132.1:p.Val119Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS099856" }, { "coordinates": [ { "allele": "T", "end": 2188, "referenceAllele": "G", "start": 2187 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "XM_017004089.1:c.361G>T" ], "proteinEffect": { "hgvs": "XP_016859578.1:p.Val121Phe", "hgvsWellDefined": "XP_016859578.1:p.Val121Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS559685" }, { "@id": "http://reg.genome.network/allele/PA113110", "coordinates": [ { "allele": "T", "end": 483, "referenceAllele": "G", "start": 482 } ], "gene": "http://reg.genome.network/gene/GN006585", "geneNCBI_id": 3973, "geneSymbol": "LHCGR", "hgvs": [ "NM_000233.4:c.430G>T" ], "proteinEffect": { "hgvs": "NP_000224.2:p.Val144Phe", "hgvsWellDefined": "NP_000224.2:p.Val144Phe" }, "referenceSequence": "http://reg.genome.network/refseq/RS662366", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000294954.12:c.430G>T" }, "RefSeq": { "hgvs": "NM_000233.4:c.430G>T" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000294954.6:p.Val144Phe" }, "RefSeq": { "hgvs": "NP_000224.2:p.Val144Phe" } } } }, { "coordinates": [ { "allele": "A", "end": 3552, "endIntronDirection": "+", "endIntronOffset": 51970, "referenceAllele": "C", "start": 3552, "startIntronDirection": "+", "startIntronOffset": 51969 } ], "gene": "http://reg.genome.network/gene/GN030651", "geneNCBI_id": 286749, "geneSymbol": "STON1-GTF2A1L", "hgvs": [ "NM_001198593.2:c.3441+51970C>A" ], "proteinEffect": { "hgvs": "NP_001185522.1:n.3441+51970C>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS713875" } ], "type": "nucleotide" }