ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5161-10A>C (rs1800718)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000118712 SCV000205289 benign not specified 2013-02-21 criteria provided, single submitter clinical testing 5161-10A>C in intron 40 of TSC2: This variant is not expected to have clinical s ignificance because it has been identified in 45.7% (2010/4396) of African Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://; dbSNP rs1800718).
PreventionGenetics,PreventionGenetics RCV000118712 SCV000305240 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000042691 SCV000395676 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282619 SCV000605463 benign none provided 2020-08-27 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000576820 SCV000677555 benign Tuberous sclerosis 2 2017-04-14 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589236 SCV000697474 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.5161-10A>C variant involves the alteration of a non-conserved intronic nucleotide with 5/5 splice prediction tools predicting no significant impact on splicing. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 24902/120464 (3635 homozygotes, 1/4), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic TSC2 variant of 1/14534 (0.0000688), suggesting this variant is likely a benign polymorphism. In addition, multiple reputable clinical laboratories cite the variant as "benign/likely benign." Therefore, the variant of interest has been classified as Benign.
Invitae RCV000576820 SCV001717662 benign Tuberous sclerosis 2 2020-12-01 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000042691 SCV000066486 not provided Tuberous sclerosis syndrome no assertion provided curation
Genetic Services Laboratory, University of Chicago RCV000118712 SCV000153127 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000118712 SCV001742344 benign not specified no assertion criteria provided clinical testing

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