ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.2979G>A (p.Thr993=)

gnomAD frequency: 0.00083  dbSNP: rs45517277
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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000125668 SCV000169130 benign not specified 2013-10-11 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000163283 SCV000213811 likely benign Hereditary cancer-predisposing syndrome 2014-11-02 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.
Invitae RCV000203727 SCV000262222 benign Tuberous sclerosis 2 2024-02-01 criteria provided, single submitter clinical testing
Preventiongenetics, part of Exact Sciences RCV000125668 SCV000305191 likely benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000043038 SCV000395621 likely benign Tuberous sclerosis syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Eurofins Ntd Llc (ga) RCV000125668 SCV000855618 likely benign not specified 2017-07-13 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000203727 SCV002039273 benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000163283 SCV002533354 benign Hereditary cancer-predisposing syndrome 2020-10-01 criteria provided, single submitter curation
CeGaT Center for Human Genetics Tuebingen RCV001530068 SCV002585532 likely benign not provided 2023-06-01 criteria provided, single submitter clinical testing TSC2: BP4, BP7, BS1
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000125668 SCV002774073 benign not specified 2021-08-03 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001530068 SCV003800144 benign not provided 2022-03-04 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000203727 SCV004016199 benign Tuberous sclerosis 2 2023-07-07 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000203727 SCV004360893 benign Tuberous sclerosis 2 2022-09-20 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000043038 SCV000066837 not provided Tuberous sclerosis syndrome no assertion provided curation
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV001530068 SCV001744644 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV001530068 SCV001920497 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000125668 SCV001972190 benign not specified no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001530068 SCV001979820 likely benign not provided no assertion criteria provided clinical testing

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