ClinVar Miner

Submissions for variant NM_001278074.1(COL5A1):c.1431G>A (p.Ala477=) (rs61729545)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124489 SCV000167922 benign not specified 2013-03-21 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 RCV000124489 SCV000302138 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000288071 SCV000478529 benign Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000473739 SCV000559962 benign Ehlers-Danlos syndrome, classic type 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588822 SCV000695384 benign not provided 2017-03-15 criteria provided, single submitter clinical testing Variant summary: The COL5A1 c.1431G>A (p.Ala477Ala) variant involves the alteration of a nucleotide, resulting in a synonymous change. 5/5 splice prediction tools predict weakening the canonical donor site, however no functional studies confirming effect of this variant on splicing have been published at the time of evaluation. This variant was found in 2210/121094 control chromosomes (208 homozygotes) at a frequency of 0.0182503, which is approximately 14600 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. Taken together, this variant is classified as benign.
Ambry Genetics RCV000617754 SCV000738354 benign Cardiovascular phenotype 2015-04-02 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;Last nucleotide of exon
Illumina Clinical Services Laboratory,Illumina RCV000473739 SCV001330480 benign Ehlers-Danlos syndrome, classic type 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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