ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4959C>T (p.Ser1653=)

gnomAD frequency: 0.01015  dbSNP: rs45517384
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Total submissions: 20
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163269 SCV000213797 benign Hereditary cancer-predisposing syndrome 2014-11-19 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 RCV000204644 SCV000262299 benign Tuberous sclerosis 2 2024-02-01 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000220474 SCV000269921 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Ser1653Ser in exon 38 of TSC2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 1.5% (127/8580) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs45517384).
Preventiongenetics, part of Exact Sciences RCV000220474 SCV000305232 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000043084 SCV000395666 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.
Athena Diagnostics Inc RCV000204644 SCV000677553 benign Tuberous sclerosis 2 2017-05-25 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586483 SCV000697472 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.4959C>T (p.Ser1653Ser) variant involves the alteration of a non-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. ESE finder predicts that this variant may affect multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 944/70720 control chromosomes (3 homozygotes) at a frequency of 0.0133484, which is approximately 194 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), suggesting this variant is likely a benign polymorphism. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000586483 SCV001156963 benign not provided 2023-11-14 criteria provided, single submitter clinical testing
GeneDx RCV000586483 SCV001833779 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000204644 SCV002039877 benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000586483 SCV002497863 benign not provided 2023-11-01 criteria provided, single submitter clinical testing TSC2: BP4, BP7, BS1, BS2
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000220474 SCV002774077 benign not specified 2022-02-07 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV000204644 SCV004016193 benign Tuberous sclerosis 2 2023-07-07 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000204644 SCV004360928 benign Tuberous sclerosis 2 2022-09-20 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000043084 SCV000066883 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055088 SCV000083306 not provided Lymphangiomyomatosis; Tuberous sclerosis syndrome no assertion provided curation
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000220474 SCV001809761 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000220474 SCV001917371 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000220474 SCV001973074 benign not specified no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000220474 SCV002037051 benign not specified no assertion criteria provided clinical testing

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