EIF3B p.Pro24=
c.72G>A · rs770420770 · VCV787313
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.66%, afr)
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 0.3 | GERP -2, phastCons 0.001 |
| Overall | ||
| CADD | 12.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.66%
African / African-American · 1,639/61,568 alleles
Filtering AF
2.55%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.51%
Overall
0.252%
2,958/1,172,694 alleles · low-frequency
exomes 1,625/1,023,276 · genomes 1,333/149,418 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.66% | 38 |
| Admixed American | 0.747% | 134 |
| Middle Eastern | 0.531% | 188 |
| Remaining individualsnot grpmax-eligible | 0.377% | 265 |
| Ashkenazi Jewishnot grpmax-eligible | 0.18% | 555 |
| European (non-Finnish) | 0.0999% | 1,001 |
| South Asian | 0.0307% | 3,261 |
| Finnishnot grpmax-eligible | 0.0187% | 5,351 |
| East Asian | 0.00411% | 24,320 |
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
- EIF3B
- Protein
- p.Pro24=
- Coding
- c.72G>A
- MANE Select
- NM_001037283
- dbSNP
- rs770420770
- Type
- single nucleotide variant
- Location
- chr7:2354993 (GRCh38)
- Gene constraint
- LOEUF 0.107 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 74.64 · 21 PDB
- Residue 24
- the 'disordered' region
Similar variants
- EIF3B p.Asn145= Benign ★★ same type
- EIF3B p.Ser64Pro Benign ★★ same type
- EIF3B c.1357-16C>T Uncertain significance ★ same type
- EIF3B p.Ala123Thr Uncertain significance ★ ⚠ same type
- EIF3B p.Ala135Pro Uncertain significance ★ ⚠ same type
- EIF3B p.Ala136Val Uncertain significance ★ ⚠ same type
- EIF3B p.Ala238Thr Uncertain significance ★ ⚠ same type
- EIF3B p.Ala246Val 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/eif3b-p-pro24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown