ClinVar Miner

Submissions for variant NM_000441.2(SLC26A4):c.1707+6T>C

dbSNP: rs727505230
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Total submissions: 2
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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 RCV000156735 SCV000206456 likely pathogenic Rare genetic deafness 2014-11-05 criteria provided, single submitter clinical testing The c.1707+6T>C variant in SLC26A4 was absent from large population studies, but has been identified by our laboratory in one individual with hearing loss and e nlarged vestibular aqueducts (EVA) who also carried a pathogenic variant on the other copy of SLC26A4. This variant is located in the 5' splice region. Computat ional tools do not suggest an impact to splicing, though this information is not predictive enough to rule out pathogenicity. However, the presence of this vari ant in combination with a reported pathogenic variant and in an individual with hearing loss and EVA, increases the likelihood that the c.1707+6T>C variant is p athogenic. In summary, although additional studies are required to fully establi sh its clinical significance, the c.1707+6T>C variant is likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV002516347 SCV003027283 uncertain significance not provided 2022-01-27 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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: 179934). This variant has been observed in individual(s) with deafness (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 15 of the SLC26A4 gene. It does not directly change the encoded amino acid sequence of the SLC26A4 protein. It affects a nucleotide within the consensus splice site.

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