ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.482-3C>T (rs1800720)

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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000118710 SCV000200860 benign not specified 2013-02-21 criteria provided, single submitter clinical testing 482-3C>T in intron 5 of TSC2: This variant is not expected to have clinical sign ificance because it has been identified in 19.1% (838/4396) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //; dbSNP rs1800720).
Ambry Genetics RCV000163048 SCV000213539 benign Hereditary cancer-predisposing syndrome 2014-11-21 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
PreventionGenetics,PreventionGenetics RCV000118710 SCV000305231 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000043224 SCV000395559 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.
Athena Diagnostics Inc RCV000576589 SCV000677551 benign Tuberous sclerosis 2 2017-04-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589095 SCV000697471 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: c.482-3C>T in TSC2 gene is an intronic change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this variant does not affect a normal splicing pattern, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.087 (10574/121392 chrs tested), predominantly in individuals of African descent (0.2; 2098/10406 chrs tested) including numerous homozygous occurrences. The observed frequencies exceed the maximum expected allele frequency for a pathogenic variant of 0.00006 suggesting that it is a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals in published reports but cited as Benign/ Likely Benign by multiple reputable databases/clinical laboratory. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000118710 SCV001156849 benign not specified 2018-07-03 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000043224 SCV000067025 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055133 SCV000083351 not provided Neoplasm of brain no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055419 SCV000083640 not provided Lymphangiomyomatosis; Tuberous sclerosis syndrome no assertion provided curation
Genetic Services Laboratory,University of Chicago RCV000118710 SCV000153125 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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