ClinVar Miner

Submissions for variant NM_001278074.1(COL5A1):c.2892C>T (p.Gly964=) (rs78511105)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124435 SCV000167868 benign not specified 2012-12-14 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.
PreventionGenetics,PreventionGenetics RCV000124435 SCV000302184 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000352863 SCV000478550 likely benign Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000467553 SCV000559970 benign Ehlers-Danlos syndrome, classic type 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587504 SCV000695392 benign not provided 2017-03-10 criteria provided, single submitter clinical testing Variant summary: The COL5A1 c.2892C>T (p.Gly964Gly) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant does not significantly affect ESE sites at the locus. However, these predictions have yet to be confirmed by functional studies. The variant does not fall within a known functional domain of the protein (InterPro). This variant was found in 5033/120846 control chromosomes (133 homozygotes) at a frequency of 0.041648, which is approximately 33318 times the estimated maximal expected allele frequency of a pathogenic COL5A1 variant (0.0000013), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. To our knowledge, the variant of interest has not been reported in affected individuals via publications and/or reputable clinical diagnostic laboratories/databases, nor has it been evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.
Ambry Genetics RCV000620060 SCV000738326 benign Cardiovascular phenotype 2015-02-25 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000467553 SCV000885239 benign Ehlers-Danlos syndrome, classic type 2018-07-30 criteria provided, single submitter clinical testing

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