ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4983C>T (p.Thr1661=) (rs35534817)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000118711 SCV000169158 benign not specified 2012-03-02 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 RCV000129657 SCV000184455 benign Hereditary cancer-predisposing syndrome 2014-12-10 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
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000118711 SCV000269922 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Thr1661Thr 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 6.8% (297/4378) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs35534817).
PreventionGenetics,PreventionGenetics RCV000118711 SCV000305234 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000042727 SCV000395668 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000587528 SCV000556618 benign not provided 2019-03-06 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000468606 SCV000677554 benign Tuberous sclerosis 2 2017-05-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587528 SCV000697473 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.4983C>T (p.Thr1661Thr) 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. 4/5 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 533/51540 control chromosomes (14 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0957862 (491/5126). This frequency is about 1393 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000118711 SCV001158895 benign not specified 2018-07-05 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000042727 SCV000066522 not provided Tuberous sclerosis syndrome no assertion provided curation
Genetic Services Laboratory, University of Chicago RCV000118711 SCV000153126 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.

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