ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.1275+3A>T

gnomAD frequency: 0.00001  dbSNP: rs370712498
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001198577 SCV001369567 uncertain significance NPHP3-related Meckel-like syndrome 2019-08-12 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence favors the pathogenic nature of this variant, however the currently available data is insufficient to conclusively support its pathogenic nature. Thus this variant is classified as Uncertain significance - favor pathogenic. The following ACMG criteria were applied in classifying this variant: PM2,PP3.
PreventionGenetics, part of Exact Sciences RCV004545119 SCV004781364 likely pathogenic NPHP3-related disorder 2023-10-27 no assertion criteria provided clinical testing The NPHP3 c.1275+3A>T variant is predicted to interfere with splicing. To our knowledge, this variant has not been reported in the literature. It has been observed in the compound heterozygous state with a NPHP3 truncating pathogenic variant in an individual with NPHP3-related disease (Internal Data, PreventionGenetics). RNA sequencing targeted variant analysis indicates this variant impacts splicing (Internal Data, PreventionGenetics). This variant is reported in 3 of ~251,000 alleles in gnomAD (http://gnomad.broadinstitute.org/variant/3-132426942-T-A). This variant is interpreted as likely pathogenic.

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