EIF4A3 p.Asp384=
c.1152C>T · rs374961147 · VCV2648396
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.108%, amr)
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 -7.6 | GERP -3.9 |
| Overall | ||
| CADD | 0.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
Admixed American · 65/60,026 alleles
Filtering AF
0.0871%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0795%
Overall
0.0302%
487/1,614,154 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.108% | 923 |
| South Asian | 0.0911% | 1,097 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| Middle Eastern | 0.033% | 3,027 |
| European (non-Finnish) | 0.0262% | 3,819 |
| East Asian | 0.0111% | 8,979 |
| African / African-American | 0.00133% | 75,020 |
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
- EIF4A3
- Protein
- p.Asp384=
- Coding
- c.1152C>T
- MANE Select
- NM_014740
- dbSNP
- rs374961147
- Type
- single nucleotide variant
- Location
- chr17:80136071 (GRCh38)
- Gene constraint
- LOEUF 0.084 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.93 · 24 PDB
- Residue 384
- the helicase c-terminal domain; an α-helix
Similar variants
- EIF4A3 p.Ala8= Benign ★★ same type
- EIF4A3 p.Lys289= Benign/Likely benign ★★ same type
- EIF4A3 p.Ser84= Benign ★★ same type
- EIF4A3 p.Thr30= Benign ★★ same type
- EIF4A3 c.587-5C>G Conflicting classifications of pathogenicity ★ same type
- EIF4A3 p.Ala13Val Uncertain significance ★ ⚠ same type
- EIF4A3 p.Ala377Asp Uncertain significance ★ ⚠ same type
- EIF4A3 p.Ala55Thr 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/eif4a3-p-asp384 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown