rs201351158
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001283009.2(RTEL1):c.3006G>A(p.Pro1002=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000946 in 1,575,202 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. P1002P) 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 -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.3006G>A | p.Pro1002= | synonymous_variant | 31/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3833G>A | non_coding_transcript_exon_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.3006G>A | p.Pro1002= | synonymous_variant | 31/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000100 AC: 15AN: 149476Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000121 AC: 30AN: 247034Hom.: 0 AF XY: 0.000171 AC XY: 23AN XY: 134466
GnomAD4 exome AF: 0.0000940 AC: 134AN: 1425604Hom.: 0 Cov.: 33 AF XY: 0.000100 AC XY: 71AN XY: 708600
GnomAD4 genome AF: 0.000100 AC: 15AN: 149598Hom.: 0 Cov.: 31 AF XY: 0.0000547 AC XY: 4AN XY: 73094
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | RTEL1: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 13, 2020 | See Variant Classification Assertion Criteria. - |
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 | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at