ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.3117G>A (p.Thr1039=) (rs747104674)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523945 SCV000621623 uncertain significance not specified 2017-10-18 criteria provided, single submitter clinical testing The c.3117 G>A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This variant is observed in 3/30778 (0.01%) alleles from individuals of South Asian background, in large population cohorts (Lek et al., 2016). Several in-silico splice prediction models predict that c.3117 G>A creates a cryptic splice acceptor site in exon 27 which may supplant the natural acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functionalstudies, the actual effect of this sequence change in this individual is unknown. Additionally, thisnucleotide substitution occurs at a position that is not conserved. Therefore, based on the currentlyavailable information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV000706187 SCV000835224 benign Tuberous sclerosis 2 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000720210 SCV000851087 likely benign History of neurodevelopmental disorder 2016-07-15 criteria provided, single submitter clinical testing Synonymous alterations with insufficient evidence to classify as benign;In silico models in agreement (benign)

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