ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4536C>T (p.Asp1512=) (rs35986575)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000118709 SCV000153124 likely benign not specified 2013-08-27 criteria provided, single submitter clinical testing
GeneDx RCV000118709 SCV000169154 benign not specified 2013-10-11 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 RCV000163349 SCV000213883 likely benign Hereditary cancer-predisposing syndrome 2014-10-14 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000118709 SCV000229773 benign not specified 2015-01-07 criteria provided, single submitter clinical testing
Invitae RCV000206462 SCV000262450 benign Tuberous sclerosis 2 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000118709 SCV000305225 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000042764 SCV000395657 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000755415 SCV000605466 benign not provided 2017-08-09 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000206462 SCV000677550 benign Tuberous sclerosis 2 2017-05-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000118709 SCV000918328 benign not specified 2018-01-02 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.4536C>T (p.Asp1512Asp) 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 ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 852/276658 control chromosomes (3 homozygotes) at a frequency of 0.0030796, which is approximately 45 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), suggesting this variant is likely a benign polymorphism. This variant has been reported in multiple affected indiviudals without strong evidence for caulsality. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Tuberous sclerosis database (TSC2) RCV000042764 SCV000066559 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055290 SCV000083510 not provided Lymphangiomyomatosis no assertion provided curation

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