ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.230+3A>G (rs1060503393)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000458530 SCV000552844 uncertain significance Juvenile polyposis syndrome 2020-06-07 criteria provided, single submitter clinical testing This sequence change falls in intron 4 of the BMPR1A gene. It does not directly change the encoded amino acid sequence of the BMPR1A protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with BMPR1A-related disease. ClinVar contains an entry for this variant (Variation ID: 411613). 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.
Color Health, Inc RCV000583478 SCV000688256 likely benign Hereditary cancer-predisposing syndrome 2017-05-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV000583478 SCV001175916 uncertain significance Hereditary cancer-predisposing syndrome 2019-07-05 criteria provided, single submitter clinical testing The c.230+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 2 in the BMPR1A gene. This nucleotide position is poorly conserved in available vertebrate species with guanine being the reference nucleotide in many species. Using the BDGP and ESEfinder splice site prediction tools, this alteration is not predicted to have any significant effect on this splice donor site; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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