ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5359G>A (p.Gly1787Ser)

gnomAD frequency: 0.00586  dbSNP: rs45517419
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Total submissions: 20
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000122242 SCV000169166 benign not specified 2013-03-03 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 RCV000130722 SCV000185609 benign Hereditary cancer-predisposing syndrome 2015-01-09 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
CSER _CC_NCGL, University of Washington RCV000054855 SCV000212204 benign Tuberous sclerosis syndrome 2015-03-11 criteria provided, single submitter research
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia RCV000202756 SCV000257720 benign Tuberous sclerosis 2 2015-03-06 criteria provided, single submitter clinical testing
Invitae RCV000202756 SCV000285462 benign Tuberous sclerosis 2 2021-12-18 criteria provided, single submitter clinical testing
Eurofins NTD LLC (GA) RCV000122242 SCV000337047 likely benign not specified 2015-11-12 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV000054855 SCV000395685 benign Tuberous sclerosis syndrome 2018-01-12 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.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000034663 SCV000609598 benign not provided 2017-05-10 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000202756 SCV000677557 benign Tuberous sclerosis 2 2017-05-30 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000034663 SCV000697479 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.5359G>A (p.Gly1787Ser) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 303/119148 control chromosomes at a frequency of 0.0025431, which is approximately 37 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV001770053 SCV002011319 uncertain significance Lymphangiomyomatosis 2021-11-03 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000202756 SCV002040291 benign Tuberous sclerosis 2 2021-11-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000034663 SCV002048124 benign not provided 2021-10-13 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000122242 SCV002070031 likely benign not specified 2021-07-26 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000130722 SCV002534061 benign Hereditary cancer-predisposing syndrome 2020-08-12 criteria provided, single submitter curation
CeGaT Center for Human Genetics Tuebingen RCV000034663 SCV002545722 benign not provided 2022-08-01 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034663 SCV000043546 probably not pathogenic not provided 2012-07-13 no assertion criteria provided research Converted during submission to Likely benign.
Tuberous sclerosis database (TSC2) RCV000054855 SCV000066425 not provided Tuberous sclerosis syndrome no assertion provided curation
ITMI RCV000122242 SCV000086466 not provided not specified 2013-09-19 no assertion provided reference population
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000034663 SCV001809584 likely benign not provided no assertion criteria provided clinical testing

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