Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 8.78%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.285 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 9.112 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.78%
African / African-American · 6,589/75,018 alleles
Filtering AF
8.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.53%
Overall
0.497%
8,019/1,614,168 alleles · common
exomes 4,145/1,461,876 · genomes 3,874/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 8.78% | 11 |
| Admixed American | 0.78% | 128 |
| Remaining individualsnot grpmax-eligible | 0.715% | 140 |
| Middle Eastern | 0.627% | 160 |
| Ashkenazi Jewishnot grpmax-eligible | 0.26% | 385 |
| South Asian | 0.034% | 2,938 |
| European (non-Finnish) | 0.0313% | 3,198 |
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
- IPO5
- Protein
- p.Arg922=
- Coding
- c.2766G>A
- MANE Select
- NM_002271
- dbSNP
- rs525939
- Type
- single nucleotide variant
- Location
- chr13:98018634 (GRCh38)
- Gene constraint
- LOEUF 0.156 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 92.12 · 3 PDB
- Residue 922
- an α-helix
Similar variants
- IPO5 p.Thr191= Benign ★★ same type
- IPO5 p.Gln8His Uncertain significance ★ ⚠ same type
- IPO5 p.Lys506Arg Uncertain significance ★ ⚠ same type
- IPO5 p.Lys775Met 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/ipo5-p-arg922 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown