ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.15297+1G>C

gnomAD frequency: 0.00003  dbSNP: rs767630412
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001048038 SCV001212027 pathogenic not provided 2024-10-08 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 70 of the USH2A 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 USH2A are known to be pathogenic (PMID: 10729113, 10909849, 20507924, 25649381). This variant is present in population databases (rs767630412, gnomAD 0.007%). Disruption of this splice site has been observed in individual(s) with retinal dystrophy and/or USH2A-related conditions (internal data). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 845053). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001075770 SCV001241402 likely pathogenic Retinal dystrophy 2019-06-26 criteria provided, single submitter clinical testing
GeneDx RCV001048038 SCV001823232 likely pathogenic not provided 2020-09-16 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele 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
Genome-Nilou Lab RCV003446597 SCV004173893 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003446597 SCV004208210 pathogenic Retinitis pigmentosa 39 2024-03-23 criteria provided, single submitter clinical testing
Natera, Inc. RCV001276140 SCV001461992 likely pathogenic Usher syndrome type 2A 2020-09-16 no assertion criteria provided clinical testing

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