ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.255C>T (p.Val85=) (rs45517098)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000125703 SCV000169168 benign not specified 2013-04-01 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 RCV000163465 SCV000214016 likely benign Hereditary cancer-predisposing syndrome 2014-10-07 criteria provided, single submitter clinical testing
Invitae RCV000203895 SCV000262488 benign Tuberous sclerosis 2 2018-01-18 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000125703 SCV000305180 benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000125703 SCV000339339 benign not specified 2016-02-12 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000042832 SCV000395553 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000203895 SCV000677540 benign Tuberous sclerosis 2 2017-05-30 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000125703 SCV000920330 benign not specified 2018-10-08 criteria provided, single submitter clinical testing Variant summary: TSC2 c.255C>T alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0011 in 235020 control chromosomes (gnomAD). The observed variant frequency is approximately 16-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in TSC2 causing Tuberous Sclerosis Complex phenotype (6.9e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.255C>T in individuals affected with Tuberous Sclerosis Complex and no experimental evidence demonstrating its impact on protein function have been reported. Four ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cites the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as benign.
Tuberous sclerosis database (TSC2) RCV000042832 SCV000066628 not provided Tuberous sclerosis syndrome no assertion provided curation

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