RTEL1 p.Asp793=
c.2379C>T · VCV4060959
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00051%, nfe)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -2.5 |
| Overall | ||
| CADD | 1.487 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00051%
European (non-Finnish) · 6/1,176,970 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000121%
Overall
0.000373%
6/1,608,258 alleles · very rare
exomes 6/1,456,036 · genomes 0/152,222 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RTEL1
- Protein
- p.Asp793=
- Coding
- c.2379C>T
- MANE Select
- NM_001283009
- Type
- single nucleotide variant
- Location
- chr20:63690407 (GRCh38)
- Gene constraint
- LOEUF 0.661 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.64 · 3 PDB
Similar variants
- RTEL1 p.Asp793Tyr Uncertain significance ★★ ⚠ same residue
- RTEL1 p.Asp793Asn Uncertain significance ★★ ⚠ same residue
- RTEL1 p.Asp793Glu Uncertain significance ★ ⚠ same residue
- RTEL1 c.1037+1G>T Likely pathogenic ★★ same condition
- RTEL1 c.2265+1G>T Likely pathogenic ★★ same condition
- RTEL1 c.2413+1G>C Pathogenic/Likely pathogenic ★★ same condition
- RTEL1 c.3110-2A>C Likely pathogenic ★★ same condition
- RTEL1 c.3110-2A>T Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rtel1-p-asp793 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown