ClinVar Miner

Submissions for variant NM_000368.5(TSC1):c.965T>C (p.Met322Thr) (rs1073123)

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Total submissions: 19
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000118695 SCV000169082 benign not specified 2013-05-24 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.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000118695 SCV000200859 benign not specified 2013-02-21 criteria provided, single submitter clinical testing Met322Thr in exon 10 of TSC1: This variant is not expected to have clinical sign ificance because it has been identified in 21.9% (967/4406) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs1073123).
Ambry Genetics RCV000162954 SCV000213441 benign Hereditary cancer-predisposing syndrome 2019-05-07 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000118695 SCV000224819 benign not specified 2014-07-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000118695 SCV000303877 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000355920 SCV000478247 benign Focal cortical dysplasia type II 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.
Illumina Clinical Services Laboratory,Illumina RCV000576638 SCV000478248 benign Tuberous sclerosis 1 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.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001282551 SCV000605459 benign none provided 2020-08-27 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000576638 SCV000677531 benign Tuberous sclerosis 1 2017-04-14 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000034613 SCV000696604 benign not provided 2016-05-26 criteria provided, single submitter clinical testing Variant summary: The TSC1 c.965T>C (p.Met322Thr) variant causes a missense change involving a non-conserved nucleotide with 3/5 in silico tools predicting a benign outcome. This variant was found in the large, broad control population, ExAC, with an allele frequency of 15658/121348 (1104 homozygotes, 1/7, frequency: 0.1290339), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic TSC1 variant of 1/40000 (0.000025), suggesting this variant is likely a benign polymorphism. In addition, multiple reputable databases/clinical laboratories cite the variant as "benign." Therefore, the variant has been classified as Benign.
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute,Kanazawa Medical University RCV000576638 SCV001430714 benign Tuberous sclerosis 1 2020-07-10 criteria provided, single submitter clinical testing
Invitae RCV000576638 SCV001722510 benign Tuberous sclerosis 1 2020-12-08 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034613 SCV000043519 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
Tuberous sclerosis database (TSC1) RCV000054853 SCV000066173 not provided Tuberous sclerosis syndrome no assertion provided curation
Tuberous sclerosis database (TSC1) RCV000054992 SCV000083210 not provided Urinary bladder cancer no assertion provided curation
Tuberous sclerosis database (TSC1) RCV000054997 SCV000083215 not provided Lymphangiomyomatosis; Tuberous sclerosis syndrome no assertion provided curation
ITMI RCV000118695 SCV000086420 not provided not specified 2013-09-19 no assertion provided reference population
Genetic Services Laboratory, University of Chicago RCV000118695 SCV000153110 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Center of Medical Genetics and Primary Health Care RCV001269358 SCV001448701 benign Malignant tumor of breast no assertion criteria provided clinical testing

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