ClinVar Miner

Submissions for variant NM_004484.4(GPC3):c.1500T>C (p.Asp500=)

gnomAD frequency: 0.06746  dbSNP: rs2314298
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000250645 SCV000310401 benign not specified criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000473514 SCV000559610 benign Wilms tumor 1 2025-02-04 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590033 SCV000698456 benign not provided 2016-05-05 criteria provided, single submitter clinical testing Variant summary: The GPC3 variant, c.1500T>C (p.Asp500Asp) causes a synonymous change involving a non-conserved nucleotide with / in silico programs via Alamut predicting no significant effect on splicing, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 2082/87736 (1/42, 182 homozygotes, 453 hemizygotes), which significantly exceeds the estimated maximum expected allele frequency for a pathogenic GPC3 variant of 1/10000000. The variant of interest, to our knowledge, has not been reported in affected individuals via publications and/or reputable databases/clinical laboratories. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.
Ambry Genetics RCV002311385 SCV000847124 benign Inborn genetic diseases 2015-10-12 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV000590033 SCV001907495 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV002257618 SCV002537446 benign Hereditary cancer-predisposing syndrome 2020-02-24 criteria provided, single submitter curation
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003316410 SCV004015744 benign Simpson-Golabi-Behmel syndrome type 1 2023-07-07 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000590033 SCV005279552 benign not provided criteria provided, single submitter not provided

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