ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1543C>T (p.Leu515=) (rs35896166)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000162956 SCV000213444 benign Hereditary cancer-predisposing syndrome 2014-10-30 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000589685 SCV000844559 benign not provided 2017-09-20 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000118699 SCV000153114 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.
Illumina Clinical Services Laboratory,Illumina RCV000055387 SCV000395582 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589685 SCV000697460 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.1543C>T (p.Leu515Leu) variant involves the alteration of a 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. However, these predictions have yet to be confirmed by functional studies. This variant was found in 293/121028 control chromosomes (3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0263918 (274/10382). This frequency is about 384 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.
Invitae RCV000204045 SCV000261873 benign Tuberous sclerosis 2 2018-01-26 criteria provided, single submitter clinical testing
Tuberous sclerosis database (TSC2) RCV000055387 SCV000083608 not provided Tuberous sclerosis syndrome no assertion provided curation

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