ClinVar Miner

Submissions for variant NM_001283009.2(RTEL1):c.1349-9G>A

gnomAD frequency: 0.00019  dbSNP: rs772899702
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000501430 SCV000596812 uncertain significance not specified 2017-01-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000651123 SCV000772973 likely benign Dyskeratosis congenita, autosomal recessive 5; Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 2024-01-11 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000501430 SCV004222790 likely benign not specified 2023-11-16 criteria provided, single submitter clinical testing Variant summary: RTEL1 c.1421-9G>A alters a non-conserved nucleotide located at a position not widely known to affect splicing. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.2e-05 in 237398 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in RTEL1 causing Dyskeratosis Congenita (Hoyeraal Hreidarsson Syndrome) (4.2e-05 vs 0.0011), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1421-9G>A in individuals affected with Dyskeratosis Congenita (Hoyeraal Hreidarsson Syndrome) and no experimental evidence demonstrating its impact on protein function have been reported. Three submitters have reported this variant to ClinVar after 2014 with conflicting assessments (likely benign, n = 2; uncertain significance, n = 1). Based on the evidence outlined above, the variant was classified as likely benign.
Natera, Inc. RCV001275092 SCV001459846 likely benign Dyskeratosis congenita, autosomal dominant 1 2020-06-13 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004541568 SCV004767815 likely benign RTEL1-related disorder 2020-10-23 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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