ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1599+5G>A (rs397515100)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000816898 SCV000957427 likely pathogenic Tuberous sclerosis 2 2018-10-25 criteria provided, single submitter clinical testing This sequence change falls in intron 15 of the TSC2 gene. It does not directly change the encoded amino acid sequence of the TSC2 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has been reported to be de novo in an individual affected with tuberous sclerosis and was also observed in a family affected with tuberous sclerosis in the Leiden Open-source Variation Database (PMID: 21520333). ClinVar contains an entry for this variant (Variation ID: 65133). Nucleotide substitutions within 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 may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. 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.
Tuberous sclerosis database (TSC2) RCV000055346 SCV000083566 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055346 SCV000083764 not provided Tuberous sclerosis syndrome no assertion provided curation

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