20-63692927-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001283009.2(RTEL1):c.2775C>T(p.Ser925Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0026 in 1,612,652 control chromosomes in the GnomAD database, including 107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001283009.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2775C>T | p.Ser925Ser | synonymous_variant | Exon 29 of 35 | 5 | NM_001283009.2 | ENSP00000353332.5 | ||
RTEL1 | ENST00000508582.7 | c.2847C>T | p.Ser949Ser | synonymous_variant | Exon 29 of 35 | 2 | ENSP00000424307.2 | |||
RTEL1 | ENST00000370018.7 | c.2775C>T | p.Ser925Ser | synonymous_variant | Exon 29 of 35 | 1 | ENSP00000359035.3 | |||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*377C>T | non_coding_transcript_exon_variant | Exon 26 of 35 | 5 | ENSP00000457428.1 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*377C>T | 3_prime_UTR_variant | Exon 26 of 35 | 5 | ENSP00000457428.1 |
Frequencies
GnomAD3 genomes AF: 0.00438 AC: 666AN: 152208Hom.: 17 Cov.: 33
GnomAD3 exomes AF: 0.00835 AC: 2087AN: 249842Hom.: 62 AF XY: 0.00650 AC XY: 881AN XY: 135614
GnomAD4 exome AF: 0.00241 AC: 3519AN: 1460326Hom.: 90 Cov.: 31 AF XY: 0.00221 AC XY: 1603AN XY: 726456
GnomAD4 genome AF: 0.00442 AC: 673AN: 152326Hom.: 17 Cov.: 33 AF XY: 0.00462 AC XY: 344AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
not specified Benign:1
- -
Inborn genetic diseases Benign:1
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
- -
RTEL1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Dyskeratosis congenita Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at