ClinVar Miner

Submissions for variant NM_206933.3(USH2A):c.1972-1G>A (rs372927796)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000672169 SCV000797246 likely pathogenic Usher syndrome, type 2A; Retinitis pigmentosa 39 2018-01-18 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001074724 SCV001240317 pathogenic Retinal dystrophy 2019-04-19 criteria provided, single submitter clinical testing
Invitae RCV001377215 SCV001574489 likely pathogenic not provided 2020-09-24 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 11 of the USH2A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with inherited retinal dystrophy (Invitae). ClinVar contains an entry for this variant (Variation ID: 556200). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). 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.
GeneDx RCV001377215 SCV001812956 pathogenic not provided 2020-01-17 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

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