ClinVar Miner

Submissions for variant NM_001278074.1(COL5A1):c.2096C>T (p.Thr699Met) (rs142313124)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000196358 SCV000249899 likely benign not specified 2017-12-28 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 RCV000302769 SCV000478541 likely benign Ehlers-Danlos syndrome, type 7A 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000468094 SCV000549016 likely benign Ehlers-Danlos syndrome, classic type 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000617228 SCV000738584 likely benign Cardiovascular phenotype 2017-09-21 criteria provided, single submitter clinical testing In silico models in agreement (benign);Subpopulation frequency in support of benign classification
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000196358 SCV000861395 likely benign not specified 2018-05-22 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000757120 SCV000885241 uncertain significance not provided 2018-05-06 criteria provided, single submitter clinical testing The COL5A1 c.2096C>T; p.Thr699Met variant (rs142313124), to our knowledge, has not been described in the medical literature but is reported as likely benign by multiple laboratories in ClinVar (Variation ID: 213040) and is observed in the general population at an overall frequency of 0.06% (172/276942 alleles) in the Genome Aggregation Database. The threonine at codon 699 is highly conserved, but computational algorithms (PolyPhen-2, SIFT) predict that this variant is tolerated. Due to limited information regarding this variant, its clinical significance cannot be determined with certainty. Pathogenic variants of COL5A1 are associated with autosomal dominant Ehlers-Danlos syndrome, classic type (MIM: 130000).
Illumina Clinical Services Laboratory,Illumina RCV000468094 SCV001328061 likely benign Ehlers-Danlos syndrome, classic type 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.
GenomeConnect, ClinGen RCV000468094 SCV000986731 not provided Ehlers-Danlos syndrome, classic type no assertion provided phenotyping only Variant interpretted as Uncertain significance and reported on 12/06/2017 by GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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