ClinVar Miner

Submissions for variant NM_001953.5(TYMP):c.215-1G>C

gnomAD frequency: 0.00004  dbSNP: rs767245071
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000599020 SCV000709896 pathogenic not provided 2024-01-29 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 16971699, 14720311, 20232099, 14757860, 21451581, 32173240, 33159497)
Counsyl RCV000018142 SCV000799642 pathogenic Mitochondrial DNA depletion syndrome 1 2018-05-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000599020 SCV001391726 pathogenic not provided 2024-01-04 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 2 of the TYMP gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in TYMP are known to be pathogenic (PMID: 9924029, 15781193). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individuals with TYMP-related conditions (PMID: 14720311, 14757860, 20232099). ClinVar contains an entry for this variant (Variation ID: 16662). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000018142 SCV004207504 pathogenic Mitochondrial DNA depletion syndrome 1 2024-03-12 criteria provided, single submitter clinical testing
OMIM RCV000018142 SCV000038421 pathogenic Mitochondrial DNA depletion syndrome 1 2004-02-01 no assertion criteria provided literature only
GeneReviews RCV000018142 SCV000264541 pathogenic Mitochondrial DNA depletion syndrome 1 2016-01-14 no assertion criteria provided literature only
GeneReviews RCV000018142 SCV000264542 pathogenic Mitochondrial DNA depletion syndrome 1 2016-01-14 no assertion criteria provided literature only
Natera, Inc. RCV001276279 SCV001462373 pathogenic Mitochondrial neurogastrointestinal encephalomyopathy 2020-09-16 no assertion criteria provided clinical testing

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