ClinVar Miner

Submissions for variant NM_000093.4(COL5A1):c.738C>T (p.Thr246=) (rs3124299)

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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 RCV000617765 SCV000738281 benign Cardiovascular phenotype 2014-12-29 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
GeneDx RCV000124481 SCV000167914 benign not specified 2012-11-13 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.
Illumina Clinical Services Laboratory,Illumina RCV000374462 SCV000478508 benign Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589836 SCV000695402 benign not provided 2017-03-15 criteria provided, single submitter clinical testing Variant summary: The COL5A1 c.738C>T (p.Thr246Thr) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. The variant is not found within a known functional domain and 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. This variant was found in 52060/121340 control chromosomes (12029 homozygotes) at a frequency of 0.4290424, which is approximately 343234 times the estimated maximal expected allele frequency of a pathogenic COL5A1 variant (0.0000013), suggesting this variant is likely a benign polymorphism. Several publications have cited the variant as a common polymorphism (Symoens_HM_2012; Takahara_AJHG_2002). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
PreventionGenetics RCV000124481 SCV000302248 benign not specified criteria provided, single submitter clinical testing

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