ClinVar Miner

Submissions for variant NM_001849.3(COL6A2):c.1674G>A (p.Ala558=) (rs144334894)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000393933 SCV000436705 likely benign Myosclerosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000303949 SCV000436706 likely benign Collagen VI-related myopathy 2018-01-13 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
GeneDx RCV000730302 SCV000619899 uncertain significance not provided 2017-08-03 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the COL6A2 gene. The c.1674 G>A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.1674 G>A variant is observed in 6/16494 (0.04%) alleles from individuals of South Asian background and in 16/65728 (0.02%) alleles from individuals of European background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Several in-silico splice prediction models predict that c.1674 G>A may create a cryptic splice acceptor site which may supplant the natural acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001081672 SCV000657118 likely benign Bethlem myopathy 1 2019-12-31 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000730302 SCV000858030 uncertain significance not provided 2017-11-14 criteria provided, single submitter clinical testing

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