ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.4397-1G>A

gnomAD frequency: 0.00009  dbSNP: rs199982344
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665749 SCV000789917 likely pathogenic Usher syndrome type 2A; Retinitis pigmentosa 39 2017-03-22 criteria provided, single submitter clinical testing
Blueprint Genetics RCV001075029 SCV001240640 likely pathogenic Retinal dystrophy 2018-03-21 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001205806 SCV001377081 likely pathogenic not provided 2023-06-14 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: 550873). Disruption of this splice site has been observed in individual(s) with retinitis pigmentosa (Invitae). This variant is present in population databases (rs199982344, gnomAD 0.03%). This sequence change affects an acceptor splice site in intron 20 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).
PreventionGenetics, part of Exact Sciences RCV004533465 SCV004117738 likely pathogenic USH2A-related disorder 2023-02-09 criteria provided, single submitter clinical testing The USH2A c.4397-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.024% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-216348825-C-T). Variants that disrupt the consensus splice acceptor site in USH2A are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Genome-Nilou Lab RCV003446295 SCV004172142 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001835072 SCV004172143 likely pathogenic Usher syndrome type 2A 2023-04-11 criteria provided, single submitter clinical testing
Baylor Genetics RCV003446295 SCV004208228 likely pathogenic Retinitis pigmentosa 39 2024-03-27 criteria provided, single submitter clinical testing
Natera, Inc. RCV001835072 SCV002093902 likely pathogenic Usher syndrome type 2A 2020-09-29 no assertion criteria provided clinical testing

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