ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.3158-7A>G

gnomAD frequency: 0.00097  dbSNP: rs201558076
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Total submissions: 6
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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 RCV000219645 SCV000271166 likely benign not specified 2015-02-26 criteria provided, single submitter clinical testing c.3158-7A>G in intron 15 of USH2A: This variant is not expected to have clinical significance because it has been identified in 0.3% (28/10558) of African chrom osomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs201558076).
GeneDx RCV000923215 SCV000534936 likely benign not provided 2020-08-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000923215 SCV001068683 benign not provided 2024-01-28 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003445707 SCV004172171 benign Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003445706 SCV004172172 benign Usher syndrome type 2A 2023-04-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000219645 SCV005185735 uncertain significance not specified 2024-05-15 criteria provided, single submitter clinical testing Variant summary: USH2A c.3158-7A>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.00016 in 1613844 control chromosomes, predominantly at a frequency of 0.0029 within the African or African-American subpopulation in the gnomAD database, including 2 homozygotes. This frequency is not significantly higher than estimated for a pathogenic variant in USH2A causing Usher Syndrome (0.00016 vs 0.011), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.3158-7A>G in individuals affected with Usher Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 228212). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

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