ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1609A>G (p.Ser537Gly)

gnomAD frequency: 0.00009  dbSNP: rs747109385
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000649767 SCV000771599 uncertain significance BAP1-related tumor predisposition syndrome 2024-01-04 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 537 of the BAP1 protein (p.Ser537Gly). This variant is present in population databases (rs747109385, gnomAD 0.07%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with BAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 539898). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Color Diagnostics, LLC DBA Color Health RCV000771524 SCV000904060 likely benign Hereditary cancer-predisposing syndrome 2020-05-15 criteria provided, single submitter clinical testing
GeneDx RCV001592812 SCV001815028 uncertain significance not provided 2023-01-10 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV000771524 SCV002703105 benign Hereditary cancer-predisposing syndrome 2023-08-08 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: 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.
Baylor Genetics RCV000649767 SCV004214888 uncertain significance BAP1-related tumor predisposition syndrome 2023-06-22 criteria provided, single submitter clinical testing

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