ClinVar Miner

Submissions for variant NM_000090.3(COL3A1):c.1188C>T (p.Gly396=) (rs745743884)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000757115 SCV000885234 uncertain significance not provided 2018-02-20 criteria provided, single submitter clinical testing The COL3A1 c.1188C>T; p.Gly396Gly variant (rs745743884; ClinVar variant ID 450335), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This synonymous variant is in a weakly conserved nucleotide, but computational analyses predict that this variant may impact splicing by creating a novel cryptic donor site (Alamut v.2.10); however, no functional studies have been performed to confirm or refute this prediction. This variant is listed in the genome Aggregation Database (gnomAD) with a South Asian population frequency of 0.04% (identified on 12 out of 30,780 chromosomes). Based on the available information, the clinical significance of the c.1188C>T cannot be determined with certainty.
Ambry Genetics RCV000618454 SCV000738516 likely benign Cardiovascular phenotype 2017-03-02 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign
Color RCV000777601 SCV000913467 likely benign Thoracic aortic aneurysm and aortic dissection 2018-08-02 criteria provided, single submitter clinical testing
GeneDx RCV000757115 SCV000618907 uncertain significance not provided 2017-07-10 criteria provided, single submitter clinical testing The c.1188 C>T (G396=) variant of uncertain significance in the COL3A1 gene has not been published as pathogenic or been reported as benign to our knowledge. This variant was observed in 3/16,430 (0.02%) alleles from individuals of South Asian ancestry in the Exome Aggregation Consortium (Lek et al., 2016). The c.1188 C>T substitution occurs at a nucleotide position that is not conserved, as thymine (T) is the wild-type nucleotide in multiple species. In silico splicing algorithms predict this variant may create a cryptic splice donor site upstream of the natural splice donor site in intron 17 of the COL3A1 gene; however, in the absence of functional mRNA studies, the physiological consequence of this variant on splicing cannot be precisely determined.

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