ClinVar Miner

Submissions for variant NM_015102.5(NPHP4):c.3996+3C>T

gnomAD frequency: 0.00013  dbSNP: rs373386232
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001891130 SCV002166246 uncertain significance Nephronophthisis 2024-12-12 criteria provided, single submitter clinical testing This sequence change falls in intron 28 of the NPHP4 gene. It does not directly change the encoded amino acid sequence of the NPHP4 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs373386232, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with NPHP4-related conditions. ClinVar contains an entry for this variant (Variation ID: 1390698). 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 is not likely to affect RNA splicing. 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.
Fulgent Genetics, Fulgent Genetics RCV002482708 SCV002793388 uncertain significance Nephronophthisis 4; Senior-Loken syndrome 4 2022-04-20 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004733399 SCV005357580 likely benign NPHP4-related disorder 2024-08-19 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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