20-63690799-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS1
The NM_001283009.2(RTEL1):c.2414-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000339 in 1,601,142 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001283009.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTEL1 | NM_001283009.2 | c.2414-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000360203.11 | |||
RTEL1-TNFRSF6B | NR_037882.1 | n.3241-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTEL1 | ENST00000360203.11 | c.2414-6C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001283009.2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00196 AC: 298AN: 152142Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000385 AC: 88AN: 228456Hom.: 0 AF XY: 0.000200 AC XY: 25AN XY: 124700
GnomAD4 exome AF: 0.000168 AC: 243AN: 1448882Hom.: 1 Cov.: 31 AF XY: 0.000132 AC XY: 95AN XY: 719958
GnomAD4 genome ? AF: 0.00197 AC: 300AN: 152260Hom.: 1 Cov.: 33 AF XY: 0.00204 AC XY: 152AN XY: 74442
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 19, 2021 | - - |
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 | - - |
RTEL1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | 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). - |
Dyskeratosis congenita Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 08, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at