ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.2580T>C (p.Phe860=) (rs13337626)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163258 SCV000213786 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000118702 SCV000228020 benign not specified 2014-10-16 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000118702 SCV000269918 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Phe860Phe in exon 23 of TSC2: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 8.7% (381/4396) of A frican American chromosomes from a broad population by the NHLBI Exome Sequencin g Project (http://evs.gs.washington.edu/EVS; dbSNP rs13337626).
PreventionGenetics,PreventionGenetics RCV000118702 SCV000305182 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000042833 SCV000395615 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 RCV000576366 SCV000677541 benign Tuberous sclerosis 2 2017-04-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587006 SCV000697464 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.2580T>C (p.Phe860Phe) variant causes a synonymous change involving a non-conserved nucleotide with 4/5 splice prediction tools predicting no significant impact on splicing and alterations to ESE binding, however, these predictions have yet to be functionally assessed. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 8679/119772 (1/13, 390 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic TSC2 variant of 1/14534, suggesting this variant is likely a benign polymorphism. In addition, multiple reputable clinical laboratories/databases cite the variant as "likely benign/benign." Therefore, the variant of interest has been classified as Benign.
Tuberous sclerosis database (TSC2) RCV000042833 SCV000066629 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055364 SCV000083585 not provided Lymphangiomyomatosis no assertion provided curation
Genetic Services Laboratory, University of Chicago RCV000118702 SCV000153117 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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