ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.1882_1885del (p.Ser628fs)

dbSNP: rs1559585778
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Color Diagnostics, LLC DBA Color Health RCV000772520 SCV000905700 pathogenic Hereditary cancer-predisposing syndrome 2020-04-21 criteria provided, single submitter clinical testing This variant deletes 4 nucleotides in exon 14 of the BAP1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in individuals affected with melanoma, colorectal cancer, renal cell carcinoma, breast cancer, and malignant mesothelioma (PMID: 24243779, 26719535). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BAP1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV001312026 SCV001502442 pathogenic not provided 2022-08-01 criteria provided, single submitter clinical testing BAP1: PVS1, PM2
Labcorp Genetics (formerly Invitae), Labcorp RCV001850964 SCV002120757 pathogenic BAP1-related tumor predisposition syndrome 2024-09-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser628Profs*8) in the BAP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BAP1 are known to be pathogenic (PMID: 21874000, 23684012). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with BAP1 tumor predisposition syndrome (PMID: 21874000, 24243779). ClinVar contains an entry for this variant (Variation ID: 628182). For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001850964 SCV000044530 pathogenic BAP1-related tumor predisposition syndrome 2011-08-28 no assertion criteria provided literature only

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