rs116057134
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001283009.2(RTEL1):c.1548C>A(p.Val516=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,470 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. V516V) 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 -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.1548C>A | p.Val516= | synonymous_variant | 18/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.2375C>A | non_coding_transcript_exon_variant | 18/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.1548C>A | p.Val516= | synonymous_variant | 18/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249444Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135584
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460470Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726522
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Dyskeratosis congenita, autosomal recessive 5;C4225346:Pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 21, 2023 | - - |
RTEL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 03, 2021 | 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