ClinVar Miner

Submissions for variant NM_000089.4(COL1A2):c.2079+3A>G

gnomAD frequency: 0.00001  dbSNP: rs1226079110
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000606996 SCV000719965 likely benign not specified 2017-06-02 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002232591 SCV001379375 uncertain significance Osteogenesis imperfecta type I; Ehlers-Danlos syndrome, classic type, 1 2024-05-23 criteria provided, single submitter clinical testing This sequence change falls in intron 34 of the COL1A2 gene. It does not directly change the encoded amino acid sequence of the COL1A2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has been observed in individual(s) with clinical features of COL1A2-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 509959). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002420611 SCV002725734 uncertain significance Cardiovascular phenotype 2020-11-20 criteria provided, single submitter clinical testing The c.2079+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 34 in the COL1A2 gene. This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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