ClinVar Miner

Submissions for variant NM_000090.4(COL3A1):c.3417+6T>C

gnomAD frequency: 0.00001  dbSNP: rs1201578152
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002040976 SCV002316451 uncertain significance Ehlers-Danlos syndrome, type 4 2021-11-29 criteria provided, single submitter clinical testing This sequence change falls in intron 46 of the COL3A1 gene. It does not directly change the encoded amino acid sequence of the COL3A1 protein. It affects a nucleotide within the consensus splice site. 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. 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 may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with COL3A1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.006%).
All of Us Research Program, National Institutes of Health RCV002040976 SCV005427373 uncertain significance Ehlers-Danlos syndrome, type 4 2024-06-09 criteria provided, single submitter clinical testing This variant causes a T to C nucleotide substitution at the +6 position of intron 46 of the COL3A1 gene. Splice site prediction tools are inconclusive regarding the impact of this variant on RNA splicing. To our knowledge, RNA studies have not been reported for this variant. This variant has not been reported in individuals affected with COL3A1-related disorders in the literature. This variant has been identified in 2/251444 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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