ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5160+3G>C

dbSNP: rs45517401
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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 RCV001852901 SCV002303073 uncertain significance Tuberous sclerosis 2 2021-05-18 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. This sequence change falls in intron 40 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 of the intron. 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. This variant has been observed in individual(s) with tuberous sclerosis complex (PMID: 16981987). ClinVar contains an entry for this variant (Variation ID: 49938). This variant is not present in population databases (ExAC no frequency).
PreventionGenetics, part of Exact Sciences RCV004528238 SCV004110010 uncertain significance TSC2-related disorder 2023-02-16 criteria provided, single submitter clinical testing The TSC2 c.5160+3G>C variant is predicted to interfere with splicing. This variant is predicted to alter splicing based on available splicing prediction programs (Alamut Visual Plus v1.6.1). However, the use of computer prediction programs is not equivalent to functional evidence. This variant has been reported in an individual with tuberous sclerosis complex (Table 2, Hung et al. 2006. PubMed ID: 16981987). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. It is interpreted as uncertain significance in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/49938/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Tuberous sclerosis database (TSC2) RCV000043205 SCV000067006 not provided Tuberous sclerosis syndrome no assertion provided curation

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