ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4570-1G>A

gnomAD frequency: 0.00001  dbSNP: rs777985056
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000824388 SCV000965284 likely benign Tuberous sclerosis 2 2024-08-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV001022719 SCV001184487 likely benign Hereditary cancer-predisposing syndrome 2023-10-05 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine RCV000824388 SCV001434941 likely pathogenic Tuberous sclerosis 2 2018-10-12 criteria provided, single submitter clinical testing This c.4570-1G>A variant in a canonical splice site acceptor site is predicted to result in a frameshift mutation resulting in a product , if any, without the GTPAse activating domain. The variant affects major biological transcripts and is consistent with loss of function disease mechanism of TSC2.The variant is absent in public databases. Therefore, this c.4570-1G>A variant in the TSC2 gene is classified as likely pathogenic.
Genome-Nilou Lab RCV000824388 SCV002040208 likely pathogenic Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
GeneDx RCV002260671 SCV002540428 uncertain significance not provided 2025-02-07 criteria provided, single submitter clinical testing Canonical splice site variant with an unclear effect on protein function, although loss of an in-frame exon is predicted; Deletions involving coding exons of this gene are a known mechanism of disease (HGMD); This variant is associated with the following publications: (PMID: 17304050, 10205261, 16199547, 18466115, 39669595, 30476936, 31447099)
Baylor Genetics RCV003461290 SCV004205111 uncertain significance Isolated focal cortical dysplasia type II 2023-01-01 criteria provided, single submitter clinical testing

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