ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.2097+5G>A

dbSNP: rs977777731
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001052272 SCV001216474 uncertain significance Tuberous sclerosis 2 2024-01-18 criteria provided, single submitter clinical testing This sequence change falls in intron 19 of the TSC2 gene. It does not directly change the encoded amino acid sequence of the TSC2 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with TSC2-related conditions. ClinVar contains an entry for this variant (Variation ID: 848502). 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.
Ambry Genetics RCV002416393 SCV002730338 uncertain significance Hereditary cancer-predisposing syndrome 2021-11-30 criteria provided, single submitter clinical testing The c.2097+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 18 in the TSC2 gene. This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV003156306 SCV003845925 uncertain significance not provided 2022-09-21 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this variant does not alter splicing; Has not been previously published as pathogenic or benign to our knowledge

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