ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.117C>G (p.Ser39=) (rs757333646)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000234488 SCV000288381 likely benign not provided 2019-02-19 criteria provided, single submitter clinical testing
GeneDx RCV000436146 SCV000534255 likely benign not specified 2016-11-28 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000574615 SCV000668300 likely benign Hereditary cancer-predisposing syndrome 2015-05-14 criteria provided, single submitter clinical testing
Color RCV000574615 SCV000682843 likely benign Hereditary cancer-predisposing syndrome 2016-06-17 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000436146 SCV000916694 likely benign not specified 2018-04-13 criteria provided, single submitter clinical testing Variant summary: BMPR1A c.117C>G alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.6e-05 (4/246138 control chromosomes). This frequency is approximately 8 fold above the estimated maximal expected allele frequency for a pathogenic variant in BMPR1A causing Juvenile Polyposis Syndrome phenotype (2e-06), suggesting that the variant is benign. To our knowledge, no occurrence of c.117C>G in individuals affected with Juvenile Polyposis Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as likely benign. Based on the evidence outlined above, the variant was classified as likely benign.

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