rs144002969
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_001283009.2(RTEL1):c.2612C>T(p.Pro871Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,612,356 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P871P) has been classified as Likely benign.
Frequency
Consequence
NM_001283009.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.2612C>T | p.Pro871Leu | missense_variant | 28/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3439C>T | non_coding_transcript_exon_variant | 28/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2612C>T | p.Pro871Leu | missense_variant | 28/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152094Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000133 AC: 33AN: 248628Hom.: 0 AF XY: 0.000126 AC XY: 17AN XY: 135076
GnomAD4 exome AF: 0.000121 AC: 177AN: 1460144Hom.: 0 Cov.: 31 AF XY: 0.000120 AC XY: 87AN XY: 726374
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74410
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 24, 2015 | - - |
Dyskeratosis congenita, autosomal recessive 5 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 12, 2018 | - - |
Dyskeratosis congenita Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jan 29, 2020 | - - |
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 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at