ClinVar Miner

Submissions for variant NM_014159.7(SETD2):c.6029C>T (p.Thr2010Ile)

gnomAD frequency: 0.00001  dbSNP: rs2041416610
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001227955 SCV001400335 benign Luscan-Lumish syndrome 2020-03-07 criteria provided, single submitter clinical testing
New York Genome Center RCV001227955 SCV002025741 uncertain significance Luscan-Lumish syndrome 2020-05-01 criteria provided, single submitter clinical testing The inherited c.6029C>T (p.Thr2010Ile) missense variant in exon 12 of 21 of SETD2 has not been reported in affected individuals in the available literature. This variant is not present in gnomAD indicating it is not a common benign variant in the populations represented in this database. In silico predictors suggest this variant is Damaging (Provean; score: -2.57) and Tolerated (SIFT; score: 0.085). Given the conflicting evidence regarding its pathogenicity, the inherited c.6029C>T (p.Thr2010Ile) variant identified in the SETD2 gene is reported as a Variant of Uncertain Significance.
GeneDx RCV003127704 SCV003803191 uncertain significance not provided 2023-02-08 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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