Submissions for variant NM_001283009.2(RTEL1):c.1992T>C (p.Asp664=)

gnomAD frequency: 0.81476  dbSNP: rs6062302

Total submissions: 12

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000454461	SCV000540225	benign	not specified	2018-03-21	criteria provided, single submitter	clinical testing	This "variant" is the major allele. The T allele is also present at a high allel e frequency (25%) and would therefore also be benign. http://gnomad.broadinstitu te.org/variant/20-62320968-T-C
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000589402	SCV000699744	benign	not provided	2017-07-10	criteria provided, single submitter	clinical testing	Variant summary: The c.2064T>C (p.Asp688=) in RTEL1 gene is a synonymous change that involves a non-conserved nucleotide. 5/5 programs in Alamut predict that this does not affect a normal splicing pattern, however no functional studies supporting these predictions were published at the time of evaluation. The variant is present in the control population dataset of ExAC at frequency of 0.749 89112/119034 chrs tested), including numerous homozygous occurrences. This frequency exceeds the estimated maximum allele frequency for a pathogenic allele in this gene (0.0011). In addition, the variant is cited as Benign/Polymorphism by a reputable database/clinical laboratory. Taking together, based on the prevalence of this variant in general population the variant was classified as Benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001519412	SCV001728278	benign	Dyskeratosis congenita, autosomal recessive 5; Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543245	SCV001761772	benign	Dyskeratosis congenita, autosomal recessive 5	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543246	SCV001761773	benign	Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3	2021-07-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000589402	SCV001960539	benign	not provided	2019-01-14	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 30462709)
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	RCV000454461	SCV004232948	benign	not specified	2024-01-24	criteria provided, single submitter	clinical testing	This variant is classified as Benign based on local population frequency. This variant was detected in 89% of patients studied by a panel of primary immunodeficiencies. Number of patients: 85. Only high quality variants are reported.
Breakthrough Genomics, Breakthrough Genomics	RCV000589402	SCV005314075	benign	not provided		criteria provided, single submitter	not provided
Natera, Inc.	RCV001272646	SCV001454885	benign	Dyskeratosis congenita	2020-09-16	no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000454461	SCV001951776	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000454461	SCV001974924	benign	not specified		no assertion criteria provided	clinical testing
GenomeConnect, ClinGen	RCV000589402	SCV002074738	not provided	not provided		no assertion provided	phenotyping only	Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing.