20-63693160-C-G
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_001283009.2(RTEL1):c.2869C>G(p.Arg957Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,459,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R957W) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001283009.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.2869C>G | p.Arg957Gly | missense_variant | 30/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3696C>G | non_coding_transcript_exon_variant | 30/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2869C>G | p.Arg957Gly | missense_variant | 30/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249160Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135292
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459956Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726274
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at