ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.4959C>T (p.Ser1653=) (rs45517384)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163269 SCV000213797 benign Hereditary cancer-predisposing syndrome 2014-11-19 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Invitae RCV000204644 SCV000262299 benign Tuberous sclerosis 2 2017-08-14 criteria provided, single submitter clinical testing
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000220474 SCV000269921 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Ser1653Ser in exon 38 of TSC2: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not located wit hin the splice consensus sequence. It has been identified in 1.5% (127/8580) of European American chromosomes from a broad population by the NHLBI Exome Sequenc ing Project (http://evs.gs.washington.edu/EVS; dbSNP rs45517384).
PreventionGenetics,PreventionGenetics RCV000220474 SCV000305232 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000043084 SCV000395666 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000204644 SCV000677553 benign Tuberous sclerosis 2 2017-05-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586483 SCV000697472 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.4959C>T (p.Ser1653Ser) 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 multiple ESE sites. However, these predictions have yet to be confirmed by functional studies. This variant was found in 944/70720 control chromosomes (3 homozygotes) at a frequency of 0.0133484, which is approximately 194 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), suggesting this variant is likely a benign polymorphism. Taken together, this variant is classified as benign.
Tuberous sclerosis database (TSC2) RCV000043084 SCV000066883 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055088 SCV000083306 not provided Lymphangiomyomatosis; Tuberous sclerosis syndrome no assertion provided curation

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