ClinVar Miner

Submissions for variant NM_001909.5(CTSD):c.294G>A (p.Thr98=)

gnomAD frequency: 0.00019  dbSNP: rs369373285
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000124641 SCV000168074 benign not specified 2013-09-26 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000706456 SCV000835505 likely benign Neuronal ceroid lipofuscinosis 2024-01-11 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001355385 SCV001550259 uncertain significance not provided no assertion criteria provided clinical testing The CTSD p.Thr98Thr variant was not identified in the literature but was identified in dbSNP (ID: rs369373285) and ClinVar (classified as benign by GeneDx and uncertain significance by Invitae). The variant was identified in control databases in 22 of 281814 chromosomes at a frequency of 0.00007807 (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 21 of 128398 chromosomes (freq: 0.000164) and African in 1 of 24862 chromosomes (freq: 0.00004), but was not observed in the Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other, or South Asian populations. The p.Thr98Thr variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. However, 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 3' splice site. However, this has not been confirmed by RNA analysis and is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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