ClinVar Miner

Submissions for variant NM_206933.4(USH2A):c.14791+5G>T

gnomAD frequency: 0.00001  dbSNP: rs1235430504
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Blueprint Genetics RCV001074063 SCV001239632 likely pathogenic Retinal dystrophy 2018-11-23 criteria provided, single submitter clinical testing
Invitae RCV002557903 SCV003524068 pathogenic not provided 2023-07-07 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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: 866233). This variant has been observed in individual(s) with Usher syndrome (PMID: 24944099). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change falls in intron 67 of the USH2A gene. It does not directly change the encoded amino acid sequence of the USH2A protein. It affects a nucleotide within the consensus splice site.
Genome-Nilou Lab RCV003446607 SCV004173896 likely pathogenic Retinitis pigmentosa 39 2023-04-11 criteria provided, single submitter clinical testing
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine RCV003448367 SCV004176703 likely pathogenic Usher syndrome type 2A 2023-03-01 criteria provided, single submitter clinical testing The invariant splice region c.14791+5G>T variant has been reported in compound heterozygous state in individuals affected with USH2A related syndrome (Baux D, et. al., 2014). The variant is reported with an allele frequency of 0.001% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Pathogenic/ Likely pathogenic. Functional studies are required to prove the pathogenicity of the variant. For these reasons, this variant has been classified as Likely Pathogenic.

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