20-63692975-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001283009.2(RTEL1):c.2823G>C(p.Glu941Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00617 in 1,612,596 control chromosomes in the GnomAD database, including 515 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001283009.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2823G>C | p.Glu941Asp | missense_variant | Exon 29 of 35 | 5 | NM_001283009.2 | ENSP00000353332.5 | ||
RTEL1 | ENST00000508582.7 | c.2895G>C | p.Glu965Asp | missense_variant | Exon 29 of 35 | 2 | ENSP00000424307.2 | |||
RTEL1 | ENST00000370018.7 | c.2823G>C | p.Glu941Asp | missense_variant | Exon 29 of 35 | 1 | ENSP00000359035.3 | |||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*425G>C | non_coding_transcript_exon_variant | Exon 26 of 35 | 5 | ENSP00000457428.1 | ||||
RTEL1-TNFRSF6B | ENST00000492259.6 | n.*425G>C | 3_prime_UTR_variant | Exon 26 of 35 | 5 | ENSP00000457428.1 |
Frequencies
GnomAD3 genomes AF: 0.0312 AC: 4741AN: 152192Hom.: 257 Cov.: 33
GnomAD3 exomes AF: 0.00798 AC: 1990AN: 249522Hom.: 105 AF XY: 0.00552 AC XY: 748AN XY: 135468
GnomAD4 exome AF: 0.00356 AC: 5194AN: 1460286Hom.: 257 Cov.: 33 AF XY: 0.00306 AC XY: 2220AN XY: 726446
GnomAD4 genome AF: 0.0312 AC: 4757AN: 152310Hom.: 258 Cov.: 33 AF XY: 0.0300 AC XY: 2235AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:3
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Dyskeratosis congenita, autosomal recessive 5;C4225346:Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
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Dyskeratosis congenita Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at