ClinVar Miner

Submissions for variant NM_000368.4(TSC1):c.1079C>A (p.Thr360Asn) (rs118203493)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163322 SCV000213850 likely benign Hereditary cancer-predisposing syndrome 2018-10-10 criteria provided, single submitter clinical testing Other data supporting benign classification;Seen in trans with a mutation or in homozygous state in individual without severe disease for that gene
PreventionGenetics,PreventionGenetics RCV000122185 SCV000303840 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001083517 SCV000478241 likely benign Tuberous sclerosis 1 2017-04-28 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Clinical Services Laboratory,Illumina RCV000404533 SCV000478242 likely benign Focal cortical dysplasia type II 2017-04-28 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.
GeneDx RCV000122185 SCV000514991 benign not specified 2018-01-10 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.
Invitae RCV001083517 SCV000562509 benign Tuberous sclerosis 1 2019-12-31 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000122185 SCV000860720 benign not specified 2018-04-13 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000122185 SCV001362454 benign not specified 2019-12-23 criteria provided, single submitter clinical testing Variant summary: TSC1 c.1079C>A (p.Thr360Asn) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00076 in 251326 control chromosomes in the gnomAD database, including 4 homozygotes. The observed variant frequency is approximately 30 fold of the estimated maximal expected allele frequency for a pathogenic variant in TSC1 causing Tuberous Sclerosis Complex phenotype (2.5e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1079C>A in individuals affected with Tuberous Sclerosis Complex and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign (n=3)/likely benign(n=2). Based on the evidence outlined above, the variant was classified as benign.
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034599 SCV000043517 variant of unknown significance not provided 2012-07-13 no assertion criteria provided research Converted during submission to Uncertain significance.
Tuberous sclerosis database (TSC1) RCV000054852 SCV000065765 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC1) RCV000054950 SCV000083166 not provided Autism spectrum disorder no assertion provided curation
ITMI RCV000122185 SCV000086402 not provided not specified 2013-09-19 no assertion provided reference population

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