ClinVar Miner

Submissions for variant NM_004656.4(BAP1):c.2056+3G>A

dbSNP: rs2153226175
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001921877 SCV002150066 uncertain significance BAP1-related tumor predisposition syndrome 2020-12-23 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals with BAP1-related conditions. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. 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. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 16 of the BAP1 gene. It does not directly change the encoded amino acid sequence of the BAP1 protein. It affects a nucleotide within the consensus splice site of the intron.
Ambry Genetics RCV002422959 SCV002727580 uncertain significance Hereditary cancer-predisposing syndrome 2022-10-21 criteria provided, single submitter clinical testing The c.2056+3G>A intronic variant results from a G to A substitution 3 nucleotides after coding exon 16 in the BAP1 gene. This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Myriad Genetics, Inc. RCV001921877 SCV005403552 likely benign BAP1-related tumor predisposition syndrome 2024-07-17 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.

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