ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.599+1G>A

dbSNP: rs45460895
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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 RCV002513622 SCV003443022 pathogenic Tuberous sclerosis 2 2022-09-27 criteria provided, single submitter clinical testing This variant is also known as Intron5+1G>A. Disruption of this splice site has been observed in individual(s) with tuberous sclerosis complex (PMID: 17304050, 21811971). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 6 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). ClinVar contains an entry for this variant (Variation ID: 49377). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site.
Tuberous sclerosis database (TSC2) RCV000042637 SCV000066432 not provided Tuberous sclerosis syndrome no assertion provided curation
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital RCV000042637 SCV000805047 pathogenic Tuberous sclerosis syndrome 2017-08-07 no assertion criteria provided clinical testing

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