ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.4086C>T (p.Ser1362=) (rs779774302)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000242483 SCV000319324 likely benign Cardiovascular phenotype 2015-09-06 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000586451 SCV000231257 uncertain significance not provided 2017-04-24 criteria provided, single submitter clinical testing
GeneDx RCV000179065 SCV000728079 likely benign not specified 2018-02-26 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.
Integrated Genetics/Laboratory Corporation of America RCV000586451 SCV000695374 uncertain significance not provided 2016-08-22 criteria provided, single submitter clinical testing Variant summary: The COL3A1 c.4086C>T (p.Ser1362Ser) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing and alterations to ESE binding, however, 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 5/121376 (1/24277), predominantly in the African cohort, 5/10404 (1/2080), which exceeds the estimated maximal expected allele frequency for a pathogenic COL3A1 variant of 1/769230. Therefore, suggesting the variant is a common polymorphism found in population(s) of African origin. However, these observations in the ExAC cohort need to be cautiously considered due to the cohort harboring individuals with a potential COL3A1 phenotype. The variant of interest, to our knowledge, has not been reported in affected individuals via publications. A reputable clinical laboratory cites the variant as "uncertain significance." Therefore, until additional information becomes available, the variant of interest has been classified as a "VUS-possibly benign."
Invitae RCV000634735 SCV000756078 likely benign Ehlers-Danlos syndrome, type 4 2017-09-11 criteria provided, single submitter clinical testing

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