ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.936+6G>A

gnomAD frequency: 0.00002  dbSNP: rs751664776
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000430432 SCV000535276 likely benign not specified 2016-12-21 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
CeGaT Center for Human Genetics Tuebingen RCV000996974 SCV001151994 likely benign not provided 2018-12-01 criteria provided, single submitter clinical testing
Invitae RCV001861638 SCV002259566 uncertain significance Developmental and epileptic encephalopathy, 12 2023-08-24 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 is not likely to affect RNA splicing. ClinVar contains an entry for this variant (Variation ID: 392070). This variant has not been reported in the literature in individuals affected with PNKP-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change falls in intron 10 of the PNKP gene. It does not directly change the encoded amino acid sequence of the PNKP protein. It affects a nucleotide within the consensus splice site.

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