ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.12295-2A>G

gnomAD frequency: 0.00002  dbSNP: rs151148854
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000041714 SCV000065410 pathogenic Rare genetic deafness 2012-08-28 criteria provided, single submitter clinical testing
Counsyl RCV000670554 SCV000795417 likely pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2017-11-14 criteria provided, single submitter clinical testing
Invitae RCV001057968 SCV001222499 pathogenic not provided 2023-09-03 criteria provided, single submitter clinical testing 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: 48392). Disruption of this splice site has been observed in individuals with clinical features of Usher syndrome (PMID: 30459346; Invitae). This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change affects an acceptor splice site in intron 62 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). For these reasons, this variant has been classified as Pathogenic.
Blueprint Genetics RCV001074339 SCV001239914 likely pathogenic Retinal dystrophy 2019-07-12 criteria provided, single submitter clinical testing
GeneDx RCV001057968 SCV001777205 pathogenic not provided 2021-05-05 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); Reported in ClinVar as pathogenic or likely pathogenic but additional evidence is not available (SCV000065410.5, SCV000795417.1; Landrum et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV003445119 SCV004173914 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001826587 SCV004173915 likely pathogenic Usher syndrome type 2A 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003445119 SCV004208246 likely pathogenic Retinitis pigmentosa 39 2024-03-21 criteria provided, single submitter clinical testing
Natera, Inc. RCV001826587 SCV002088313 pathogenic Usher syndrome type 2A 2021-06-08 no assertion criteria provided clinical testing

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