20-63688003-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001283009.2(RTEL1):c.1548C>T(p.Val516=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000708 in 1,612,822 control chromosomes in the GnomAD database, including 6 homozygotes. 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.1548C>T | p.Val516= | synonymous_variant | 18/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.2375C>T | non_coding_transcript_exon_variant | 18/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.1548C>T | p.Val516= | synonymous_variant | 18/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00400 AC: 609AN: 152234Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.000998 AC: 249AN: 249444Hom.: 1 AF XY: 0.000708 AC XY: 96AN XY: 135584
GnomAD4 exome AF: 0.000364 AC: 531AN: 1460470Hom.: 3 Cov.: 33 AF XY: 0.000300 AC XY: 218AN XY: 726522
GnomAD4 genome AF: 0.00401 AC: 611AN: 152352Hom.: 3 Cov.: 33 AF XY: 0.00385 AC XY: 287AN XY: 74506
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 03, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
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 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at