ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.1342+5G>A (rs878854663)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000229003 SCV000288385 uncertain significance Juvenile polyposis syndrome 2016-02-25 criteria provided, single submitter clinical testing This variant affects a highly conserved nucleotide within the consensus splice site of intron 11. The majority of introns (75%) have a G at this position (PMID: 9536098). This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a BMPR1A-related disease. Nucleotide substitutions at +5 position of the intron are relatively common causes of aberrant splicing (PMID: 17576681) but according to multiple splice site algorithms this particular variant is not predicted to significantly affect splicing. These predictions have not been confirmed by published functional studies. In summary, this is a novel intronic change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance.
GeneDx RCV000235736 SCV000293774 uncertain significance not provided 2015-12-28 criteria provided, single submitter clinical testing This variant is denoted BMPR1A c.1342+5G>A or IVS11+5G>A and consists of a G>A nucleotide substitution at the +5 position of intron 11 of the BMPR1A gene. Multiple in silico models predict this variant to destroy the nearby natural donor site, and to possibly cause abnormal gene splicing; however, in the absence of RNA or functional studies, the actual effect of this variant is unknown. This variant has not, to our knowledge, been published in the literature as pathogenic or benign. BMPR1A c.1342+5G>A was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. The guanine (G) nucleotide that is altered is not conserved across species. Based on currently available information, it is unclear whether BMPR1A c.1342+5G>A is pathogenic or benign.

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