ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.289C>T (p.Arg97Cys)

gnomAD frequency: 0.00001  dbSNP: rs768671254
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000863850 SCV001004572 likely benign Ehlers-Danlos syndrome, type 4 2023-08-17 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV001189197 SCV001356438 likely benign Familial thoracic aortic aneurysm and aortic dissection 2020-07-22 criteria provided, single submitter clinical testing
GeneDx RCV001772159 SCV002002218 uncertain significance not provided 2022-02-14 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function; Not located in the triple helical region, where the majority of pathogenic missense variants occur (HGMD)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003489947 SCV004242140 likely benign not specified 2023-12-11 criteria provided, single submitter clinical testing Variant summary: COL3A1 c.289C>T (p.Arg97Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 250826 control chromosomes. The observed variant frequency is approximately 92 fold of the estimated maximal expected allele frequency for a pathogenic variant in COL3A1 causing Aortopathy phenotype (1.3e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.289C>T in individuals affected with Aortopathy and no experimental evidence demonstrating its impact on protein function have been reported. Three submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as likely benign (n=2) and VUS (n=1). Based on the evidence outlined above, the variant was classified as likely benign.

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