ClinVar Miner

Submissions for variant NM_004329.3(BMPR1A):c.676-3A>C

gnomAD frequency: 0.00001  dbSNP: rs587782760
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000132281 SCV000187365 likely benign Hereditary cancer-predisposing syndrome 2019-10-09 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.
Counsyl RCV000412020 SCV000488174 uncertain significance Generalized juvenile polyposis/juvenile polyposis coli 2016-01-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001358779 SCV000552897 likely benign Juvenile polyposis syndrome 2025-01-20 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000132281 SCV000906002 likely benign Hereditary cancer-predisposing syndrome 2020-12-11 criteria provided, single submitter clinical testing
GeneDx RCV001588990 SCV001827186 uncertain significance not provided 2019-10-09 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes splice predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Nucleotide substitution has no predicted effect on splicing and is not conserved across species; Observed in individuals with breast cancer (Desmond 2015, Tung 2016); This variant is associated with the following publications: (PMID: 26976419, 26270727)
Myriad Genetics, Inc. RCV001358779 SCV004019491 likely benign Juvenile polyposis syndrome 2023-03-02 criteria provided, single submitter clinical testing This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.
All of Us Research Program, National Institutes of Health RCV001358779 SCV004818133 likely benign Juvenile polyposis syndrome 2023-11-02 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004730880 SCV005335994 uncertain significance BMPR1A-related disorder 2024-06-18 no assertion criteria provided clinical testing The BMPR1A c.676-3A>C variant is predicted to interfere with splicing. This variant was reported in individuals with breast cancer and melanoma (Desmond et al. 2015. PubMed ID: 26270727; Table A2. Tung N et al. 2016. PubMed ID: 26976419). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations regarding its pathogenicity in ClinVar, ranging from likely benign to uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/142843/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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