20-63694385-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001283009.2(RTEL1):c.3006G>C(p.Pro1002=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000127 in 1,575,082 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.3006G>C | p.Pro1002= | synonymous_variant | 31/35 | ENST00000360203.11 | |
RTEL1-TNFRSF6B | NR_037882.1 | n.3833G>C | non_coding_transcript_exon_variant | 31/38 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.3006G>C | p.Pro1002= | synonymous_variant | 31/35 | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000669 AC: 1AN: 149476Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000405 AC: 1AN: 247034Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134466
GnomAD4 exome AF: 7.01e-7 AC: 1AN: 1425606Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 708600
GnomAD4 genome ? AF: 0.00000669 AC: 1AN: 149476Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 72966
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 | Sep 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at