ClinVar Miner

Submissions for variant NM_024753.5(TTC21B):c.3102-2A>G

gnomAD frequency: 0.00001  dbSNP: rs779472675
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV001535854 SCV001752467 likely pathogenic Asphyxiating thoracic dystrophy 4; Nephronophthisis 12 2021-06-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003771652 SCV004591333 likely pathogenic Jeune thoracic dystrophy; Nephronophthisis 2024-01-04 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 23 of the TTC21B 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 TTC21B are known to be pathogenic (PMID: 18327258, 21068128, 21258341, 23559409, 24876116, 25492405, 27491411, 29068549). This variant is present in population databases (rs779472675, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with TTC21B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1179039). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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