ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1543C>T (p.Leu515=)

gnomAD frequency: 0.00749  dbSNP: rs35896166
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 15
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118699 SCV000153114 benign not specified 2021-06-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV000162956 SCV000213444 benign Hereditary cancer-predisposing syndrome 2014-10-30 criteria provided, single submitter clinical testing This alteration is classified as 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 RCV001081735 SCV000261873 benign Tuberous sclerosis 2 2024-02-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000055387 SCV000395582 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000589685 SCV000697460 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.1543C>T (p.Leu515Leu) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 293/121028 control chromosomes (3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0263918 (274/10382). This frequency is about 384 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), indicating this is a benign polymorphism found primarily in the populations of African origin. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Athena Diagnostics Inc RCV000589685 SCV000844559 benign not provided 2017-09-20 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589685 SCV001159970 benign not provided 2023-09-18 criteria provided, single submitter clinical testing
GeneDx RCV000589685 SCV001849408 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001081735 SCV002041350 benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000118699 SCV002774061 benign not specified 2021-10-14 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002496739 SCV002807364 likely benign Lymphangiomyomatosis; Isolated focal cortical dysplasia type II; Tuberous sclerosis 2 2021-07-23 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV001081735 SCV004016122 benign Tuberous sclerosis 2 2023-07-07 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000055387 SCV000083608 not provided Tuberous sclerosis syndrome no assertion provided curation
Clinical Genetics, Academic Medical Center RCV000118699 SCV001921592 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000118699 SCV001970863 benign not specified no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.