ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.2056C>G (p.Pro686Ala) (rs41263775)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000417377 SCV000233331 likely benign not specified 2017-12-29 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 RCV000181055 SCV000319463 likely benign Cardiovascular phenotype 2018-03-19 criteria provided, single submitter clinical testing Insufficient or conflicting evidence;In silico models in agreement (benign);Subpopulation frequency in support of benign classification
Invitae RCV001081847 SCV000554694 benign Ehlers-Danlos syndrome, type 4 2019-12-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000417377 SCV000603133 likely benign not specified 2016-08-22 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588360 SCV000695364 benign not provided 2016-08-22 criteria provided, single submitter clinical testing Variant summary: The COL3A1 c.2056C>G (p.Pro686Ala) variant causes a missense change involving a non-conserved nucleotide with 2/3 in silico tools (SNPs&GO and MutationTaster not captured here due to low relability index and p-value, respectively) predict a "benign" outcome, although these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 33/36436 (1/1104), predominantly in the African cohort, 33/3964 (1/120), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic COL3A1 variant of 1/769230. Therefore, suggesting the variant of interest is a common polymorphism found in population(s) of African origin. The variant of interest, to our knowledge, has not been reported in affected individuals via publications, while one reputable clinical laboratory cites the variant as "likely benign." Therefore, the variant of interest has been classified as Benign.
Color RCV001185496 SCV001351721 benign Familial thoracic aortic aneurysm and aortic dissection 2018-11-16 criteria provided, single submitter clinical testing

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