ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.1190-2A>G

gnomAD frequency: 0.00001  dbSNP: rs200818935
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523813 SCV000619018 pathogenic not provided 2019-08-10 criteria provided, single submitter clinical testing Canonical splice site variant in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001378303 SCV001575848 likely pathogenic Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis 2023-06-07 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 450433). This variant has not been reported in the literature in individuals affected with CEP290-related conditions. This variant is present in population databases (rs200818935, gnomAD 0.005%). This sequence change affects an acceptor splice site in intron 13 of the CEP290 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CEP290 are known to be pathogenic (PMID: 16909394, 17345604, 20690115).
Baylor Genetics RCV003470653 SCV004214866 likely pathogenic Bardet-Biedl syndrome 14 2024-03-09 criteria provided, single submitter clinical testing

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