ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.3228C>T (p.Pro1076=) (rs200917999)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000434555 SCV000515411 likely benign not specified 2015-11-11 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 RCV000618368 SCV000738547 likely benign Cardiovascular phenotype 2017-03-20 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign
Color RCV000772006 SCV000904962 likely benign Familial thoracic aortic aneurysm and aortic dissection 2018-09-04 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000434555 SCV000919239 benign not specified 2017-10-10 criteria provided, single submitter clinical testing Variant summary: The COL3A1 c.3228C>T (p.Pro1076Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 12/246140 control chromosomes, predominantly observed in the Ashkenazi Jewish subpopulation at a frequency of 0.000508 (5/9846). This frequency is about 406 times the estimated maximal expected allele frequency of a pathogenic COL3A1 variant (0.0000013), suggesting this is likely a benign polymorphism found primarily in the populations of Ashkenazi Jewish origin. In addition, one other clinical diagnostic laboratory classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications, nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Invitae RCV000868526 SCV001009866 likely benign Ehlers-Danlos syndrome, type 4 2019-12-31 criteria provided, single submitter clinical testing

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