ATRIP c.671+20del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00135%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +20 | near-intronic (+20 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 0.63 | GERP 0.87, phastCons 0.002 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00135%
African / African-American · 1/74,034 alleles
Overall
7.05e-05%
1/1,417,976 alleles · very rare
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
- ATRIP
- Coding
- c.671+20del
- MANE Select
- NM_130384
- dbSNP
- rs778826984
- Type
- Deletion
- Location
- chr3:48454436 (GRCh38)
- Gene constraint
- LOEUF 0.707 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 70.10 · 24 PDB
Similar variants
- TREX1 p.Ala139fs Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Ile207fs Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Pro212fs Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Pro290_Ala295del Pathogenic/Likely pathogenic ★★ same type
- TREX1 p.Thr49fs Pathogenic/Likely pathogenic ★★ same type
- ATRIP p.Leu496_Leu497del Uncertain significance ★★ same type
- ATRIP p.Thr384_Gly385insTer Uncertain significance ★★ same type
- TREX1 p.Tyr305fs Uncertain significance ★★ same type
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/atrip-c-671-plus-20del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown