ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.292C>T (p.Arg98Trp)

gnomAD frequency: 0.00004  dbSNP: rs372321790
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000989413 SCV000556682 benign Tuberous sclerosis 2 2023-12-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV000573567 SCV000664696 likely benign Hereditary cancer-predisposing syndrome 2021-04-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
Mendelics RCV000989413 SCV001139735 benign Tuberous sclerosis 2 2019-05-28 criteria provided, single submitter clinical testing
GeneDx RCV001555447 SCV001776870 uncertain significance not provided 2020-03-11 criteria provided, single submitter clinical testing Reported in a deceased fetus with TSC who may have had a deletion of the TSC2 gene on the opposite allele (in trans); inherited from an unaffected mother (Coevoets et al., 2009); Published functional studies suggest the variant may have a damaging effect (Coevoets et al., 2009; Hoogeveen-Westerveld et al., 2011); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25637381, 18854862, 21309039)
Genome-Nilou Lab RCV000989413 SCV002041050 likely benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV001555447 SCV004221425 uncertain significance not provided 2014-10-13 criteria provided, single submitter clinical testing In the published literature, this variant has been reported in an individual with renal cell carcinoma (PMID: 35441217 (2022)). The variant was also reported in a fetus with tuberous sclerosis who also carried a gross deletion in the TSC2 gene (PMID: 18854862 (2009)). Assessment of experimental analysis yielded inconclusive results regarding the impact of this variant on protein function (PMID: 18854862 (2009), 21309039 (2011)). The frequency of this variant in the general population, 0.00016 (5/31024 chromosomes in Latino/Admixed American subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.
Tuberous sclerosis database (TSC2) RCV000055443 SCV000083664 not provided Tuberous sclerosis syndrome no assertion provided curation
CSER _CC_NCGL, University of Washington RCV000055443 SCV000190664 likely benign Tuberous sclerosis syndrome 2014-06-01 no assertion criteria provided research

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