chr20-63694435-A-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001283009.2(RTEL1):āc.3056A>Gā(p.Gln1019Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000674 in 1,611,978 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q1019E) has been classified as Uncertain significance.
Frequency
Consequence
NM_001283009.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.3056A>G | p.Gln1019Arg | missense_variant | 31/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3883A>G | non_coding_transcript_exon_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.3056A>G | p.Gln1019Arg | missense_variant | 31/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00296 AC: 450AN: 151928Hom.: 2 Cov.: 31
GnomAD3 exomes AF: 0.000996 AC: 246AN: 246902Hom.: 4 AF XY: 0.000759 AC XY: 102AN XY: 134410
GnomAD4 exome AF: 0.000438 AC: 640AN: 1459932Hom.: 5 Cov.: 33 AF XY: 0.000413 AC XY: 300AN XY: 726170
GnomAD4 genome AF: 0.00294 AC: 447AN: 152046Hom.: 2 Cov.: 31 AF XY: 0.00276 AC XY: 205AN XY: 74344
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jun 23, 2017 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | RTEL1: BP4, BS1, BS2 - |
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 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at