ClinVar Miner

Submissions for variant NM_001278074.1(COL5A1):c.3855C>T (p.Gly1285=) (rs139544503)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124441 SCV000167874 benign not specified 2013-05-24 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.
Invitae RCV001507137 SCV000283489 benign Ehlers-Danlos syndrome, classic type I 2020-11-27 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000124441 SCV000302204 likely benign not specified criteria provided, single submitter clinical testing
Ambry Genetics RCV000250634 SCV000319629 likely benign Cardiovascular phenotype 2015-05-20 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000755497 SCV000603190 likely benign not provided 2017-10-10 criteria provided, single submitter clinical testing The c.3855C>T variant has not been previously associated with any aortopathy or connective tissue disorder and is listed in the ClinVar database as likely benign or benign (Variation ID: 136882). This variant is rare in the general population, and is listed in the Genome Aggregation Database (gnomAD) browser with a frequency in non-Finnish European populations of 0.14% (identified in 102 out of 71,872 chromosomes). However, this variant affects a weakly conserved nucleotide (Alamut software v 2.8.1), does not alter the amino acid sequence of COL5A1 protein, and is not predicted to alter natural COL5A1 mRNA splicing (Alamut software v 2.8.1). Therefore, c.3855C>T variant is likely to be benign.
Illumina Clinical Services Laboratory,Illumina RCV001085673 SCV001328143 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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