ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1727C>T (p.Thr576Ile)

gnomAD frequency: 0.00006  dbSNP: rs374920141
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000773174 SCV000906731 likely benign Hereditary cancer-predisposing syndrome 2016-07-25 criteria provided, single submitter clinical testing
Invitae RCV000796507 SCV000936025 uncertain significance BAP1-related tumor predisposition syndrome 2024-01-31 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 576 of the BAP1 protein (p.Thr576Ile). This variant is present in population databases (rs374920141, gnomAD 0.01%). This missense change has been observed in individual(s) with uveal melanoma (PMID: 26876698). ClinVar contains an entry for this variant (Variation ID: 628615). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.
Ambry Genetics RCV000773174 SCV002716672 likely benign Hereditary cancer-predisposing syndrome 2022-01-06 criteria provided, single submitter clinical testing This alteration is classified as likely 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.

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