ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4990-1G>A

dbSNP: rs1555439650
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000516408 SCV000615917 pathogenic not provided 2016-11-09 criteria provided, single submitter clinical testing
Invitae RCV001851471 SCV002281861 likely pathogenic Tuberous sclerosis 2 2023-09-06 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 38 of the TSC2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TSC2 are known to be pathogenic (PMID: 10205261, 17304050). 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: 448734). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
GeneDx RCV000516408 SCV002522082 pathogenic not provided 2022-05-27 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; Also known as IVS37-1G>A
Revvity Omics, Revvity Omics RCV001851471 SCV003810277 likely pathogenic Tuberous sclerosis 2 2021-01-21 criteria provided, single submitter clinical testing

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