ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.5383C>T (p.Arg1795Cys) (rs45517423)

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Total submissions: 17
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163344 SCV000213878 likely benign Hereditary cancer-predisposing syndrome 2019-03-12 criteria provided, single submitter clinical testing Intact protein function observed in appropriate functional assay(s);Other data supporting benign classification;Co-occurence with a mutation in another gene that clearly explains a proband's phenotype
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000178483 SCV000230568 likely benign not specified 2014-07-15 criteria provided, single submitter clinical testing
GeneDx RCV000178483 SCV000243618 benign not specified 2014-08-14 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.
Genetic Services Laboratory,University of Chicago RCV000178483 SCV000249208 uncertain significance not specified 2015-06-23 criteria provided, single submitter clinical testing
Invitae RCV000989443 SCV000261971 benign Tuberous sclerosis 2 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000054862 SCV000395686 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.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000034665 SCV000511761 likely benign not provided 2016-11-30 criteria provided, single submitter clinical testing Converted during submission to Likely benign.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000178483 SCV000540604 likely benign not specified 2017-01-24 criteria provided, single submitter clinical testing Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is classified in HGMD as DM and seen in 7 papers, including in patients who inherited the mutation from unaffected parents. This variant is present in gnomAD with a Max MAF of 0.36% of Ashkenazi Jews (36/10110 chrs and homozygous in 1 Latino). High for tuberous sclerosis incidence of 1/25000-1/11300. The variant is classified with 1 star in ClinVar as VUS by 3 submitters (CSER_CC_NCGL, University of Chicago, and Ambry), Likely benign by 3 submitters (Emory, Invitae, Biesecker), and Benign by GeneDx.
Athena Diagnostics Inc RCV000034665 SCV000844592 benign not provided 2017-12-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000178483 SCV000884758 likely benign not specified 2019-06-27 criteria provided, single submitter clinical testing
Mendelics RCV000989443 SCV001139769 benign Tuberous sclerosis 2 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000034665 SCV001150727 uncertain significance not provided 2017-03-01 criteria provided, single submitter clinical testing
Centre for Mendelian Genomics,University Medical Centre Ljubljana RCV001197128 SCV001367764 benign Neurodevelopmental disorder 2019-03-27 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence on this varinat's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP3. This variant was detected in heterozygous state.
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034665 SCV000043548 probably not pathogenic not provided 2012-07-13 no assertion criteria provided research Converted during submission to Likely benign.
Tuberous sclerosis database (TSC2) RCV000054862 SCV000067067 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC2) RCV000055245 SCV000083464 not provided Lymphangiomyomatosis; Tuberous sclerosis syndrome no assertion provided curation
CSER _CC_NCGL, University of Washington RCV000148917 SCV000190670 uncertain significance Tuberous sclerosis and lymphangiomyomatosis 2014-06-01 no assertion criteria provided research

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