20-63692813-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001283009.2(RTEL1):c.2661C>T(p.Pro887=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00153 in 1,610,740 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P887P) has been classified as Likely benign.
Frequency
Consequence
NM_001283009.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.2661C>T | p.Pro887= | synonymous_variant | 29/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3488C>T | non_coding_transcript_exon_variant | 29/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2661C>T | p.Pro887= | synonymous_variant | 29/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00112 AC: 171AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00114 AC: 284AN: 248680Hom.: 0 AF XY: 0.000961 AC XY: 130AN XY: 135224
GnomAD4 exome AF: 0.00158 AC: 2298AN: 1458424Hom.: 4 Cov.: 30 AF XY: 0.00151 AC XY: 1094AN XY: 725168
GnomAD4 genome AF: 0.00112 AC: 171AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000994 AC XY: 74AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2023 | RTEL1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 05, 2021 | - - |
Dyskeratosis congenita Benign:2
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 10, 2019 | - - |
Likely benign, criteria provided, single submitter | curation | Sema4, Sema4 | Sep 03, 2021 | - - |
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 14, 2022 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 30, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Dyskeratosis congenita, autosomal recessive 5;C4225346:Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
RTEL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 01, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at