ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.3889G>A (p.Ala1297Thr) (rs45517319)

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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000129666 SCV000184464 benign Hereditary cancer-predisposing syndrome 2014-12-09 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000122229 SCV000229650 benign not specified 2015-01-02 criteria provided, single submitter clinical testing
GeneDx RCV000122229 SCV000243587 likely benign not specified 2017-09-27 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 RCV000034653 SCV000285372 benign not provided 2019-03-06 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000231518 SCV000296950 benign Tuberous sclerosis 2 2015-11-10 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000122229 SCV000305209 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000054864 SCV000395636 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000122229 SCV000605469 benign not specified 2019-05-09 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000231518 SCV000677543 benign Tuberous sclerosis 2 2017-05-24 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000034653 SCV000697465 benign not provided 2016-08-23 criteria provided, single submitter clinical testing Variant summary: The TSC2 c.3889G>A (p.Ala1297Thr) variant involves the alteration of a conserved nucleotide. 2/3 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 193/33944 control chromosomes at a frequency of 0.0056858, which is approximately 83 times the estimated maximal expected allele frequency of a pathogenic TSC2 variant (0.0000688), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Center for Human Genetics, Inc RCV000231518 SCV000782408 uncertain significance Tuberous sclerosis 2 2016-11-01 criteria provided, single submitter clinical testing
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000034653 SCV000043536 probably not pathogenic not provided 2012-07-13 no assertion criteria provided research Converted during submission to Likely benign.
Tuberous sclerosis database (TSC2) RCV000054864 SCV000066967 not provided Tuberous sclerosis syndrome no assertion provided curation
ITMI RCV000122229 SCV000086451 not provided not specified 2013-09-19 no assertion provided reference population

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