ClinVar Miner

Submissions for variant NM_007294.4(BRCA1):c.5406+2T>G

dbSNP: rs2051071309
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Brotman Baty Institute, University of Washington RCV001077329 SCV001243243 not provided Breast-ovarian cancer, familial, susceptibility to, 1 no assertion provided in vitro
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV001077329 SCV003927200 likely pathogenic Breast-ovarian cancer, familial, susceptibility to, 1 2023-05-05 no assertion criteria provided clinical testing The BRCA1 mutation detected in this specimen (c.5406+2T>G) show sequence change affects a splice site in intron area after exon 22 of the BRCA1 gene . It is expected to disrupt RNA splicing and likely results in an absent or disrupts protein product . This variant is previously reported (PMID: 25329591) associated with breast cancer. ClinVar has an entry for this variant (ID:868431). This variant is also known as c.5469+2T>G. Donor and acceptor splice site variants typically lead to disrupt protein and loss of function. A functional study (PMID: 25329591) shows this variant results in loss of function. The saturation genome editing (SGE) assay for BRCA1 NM_007294.3:c.5406+2T>G, a CANONICAL SPLICE variant, produced a function score of -1.44, corresponding to a functional classification of LOSS_OF_FUNCTION. This variant is not found in gnomAD genomes. In-silico predictions show Pathogenic computational verdict based on 6 pathogenic predictions from BayesDel_addAF, DANN, EIGEN, FATHMM-MKL, MutationTaster and scSNV-Splicing vs no benign predictions. Therefore, this variant has been classified as Likely pathogenic.

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