ClinVar Miner

Submissions for variant NM_000368.4(TSC1):c.106+15A>G (rs80258442)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000125622 SCV000169079 benign not specified 2013-10-14 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.
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000125622 SCV000269915 benign not specified 2013-02-21 criteria provided, single submitter clinical testing 106+15A>G in intron 3 of TSC1: This variant is not expected to have clinical sig nificance because it is not located within the conserved splice consensus sequen ce. It has been identified in 9.6% (17/178) of Japanese chromosomes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.nih.gov/projects/SN P; dbSNP rs80258442).
PreventionGenetics,PreventionGenetics RCV000125622 SCV000303839 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000041984 SCV000478267 likely benign Tuberous sclerosis syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000397239 SCV000478268 likely benign Focal cortical dysplasia type II 2016-06-14 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589338 SCV000696598 benign not provided 2016-05-26 criteria provided, single submitter clinical testing Variant summary: The TSC1 c.106+15A>G variant involves the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a benign outcome for this variant along with 5/5 in silico splice prediction tools predicting the variant not to have an impact on normal splicing. This variant was found in 630/119968 control chromosomes (26 homozygotes), predominantly observed in the East Asian subpopulation (25 homozygotes) at a frequency of 0.0705565 (601/8518). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic TSC1 variant (0.000025), suggesting this is likely a benign polymorphism found primarily in populations of East Asian origin. In addition, one clinical diagnostic laboratory classified this variant as Benign. Taken together, this variant is classified as Benign.
Tuberous sclerosis database (TSC1) RCV000041984 SCV000065763 not provided Tuberous sclerosis syndrome no assertion provided curation

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