ClinVar Miner

Submissions for variant NM_000368.4(TSC1):c.3103G>A (p.Gly1035Ser) (rs118203742)

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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000122196 SCV000169096 benign not specified 2013-10-01 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 RCV000130763 SCV000185655 benign Hereditary cancer-predisposing syndrome 2014-12-03 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Genetic Services Laboratory, University of Chicago RCV000122196 SCV000249203 uncertain significance not specified 2014-11-11 criteria provided, single submitter clinical testing
Invitae RCV001080484 SCV000261866 benign Tuberous sclerosis 1 2020-12-07 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000122196 SCV000303868 likely benign not specified criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000122196 SCV000333780 likely benign not specified 2015-08-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000297382 SCV000478183 likely benign Focal cortical dysplasia type II 2018-09-25 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV001080484 SCV000478184 likely benign Tuberous sclerosis 1 2018-09-25 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000034609 SCV000696608 benign not provided 2016-08-31 criteria provided, single submitter clinical testing Variant Summary: The c.3103G>A (p.Gly1035Ser) in TSC1 gene is a missense change that involves a non-conserved nucleotide and 3/4 in silico programs predicting a "benign" outcome. The variant of interest was observed in controls with an allele frequency of 0.0014 (170/119052chrs tested) which exceeds the predicted maximum expected allele frequency for a pathogenic variant in this gene (0.0025). The variant of interest has been reported in multiple affected individuals in cis with a pathogenic variant (Nellist, 2009, TSC1 db).In the functional studies the G1035S had similar activities as wt (Nellist, 2009). In addition, multiple reputable databases/clinical laboratories and publications cite the variant with a classification of "Neutral/likely benign." Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as a Benign.
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034609 SCV000043507 probably not pathogenic not provided 2012-07-13 no assertion criteria provided research Converted during submission to Likely benign.
Tuberous sclerosis database (TSC1) RCV000054850 SCV000066052 not provided Tuberous sclerosis syndrome no assertion provided curation
ITMI RCV000122196 SCV000086415 not provided not specified 2013-09-19 no assertion provided reference population
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000034609 SCV001743145 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000034609 SCV001807484 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics,Academic Medical Center RCV000034609 SCV001922843 likely benign not provided no assertion criteria provided clinical testing

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