EEF1D p.Ala99=
c.297G>A · rs61757370 · VCV780132
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.61%, 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 -6.9 | GERP -3.1 |
| Overall | ||
| CADD | 1.104 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.61%
African / African-American · 3,388/73,438 alleles
Filtering AF
4.48%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.43%
Overall
0.319%
5,011/1,572,256 alleles · low-frequency
exomes 2,911/1,419,900 · genomes 2,100/152,356 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.61% | 22 |
| Middle Eastern | 0.939% | 107 |
| Admixed American | 0.61% | 164 |
| Remaining individualsnot grpmax-eligible | 0.502% | 199 |
| Ashkenazi Jewishnot grpmax-eligible | 0.471% | 213 |
| European (non-Finnish) | 0.0688% | 1,454 |
| South Asian | 0.0142% | 7,062 |
| East Asian | 0.00225% | 44,460 |
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
- EEF1D
- Protein
- p.Ala99=
- Coding
- c.297G>A
- MANE Select
- NM_001130053
- dbSNP
- rs61757370
- Type
- single nucleotide variant
- Location
- chr8:143589785 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 4 PDB
- Residue 99
- the 'leucine-zipper' region
Similar variants
- EEF1D c.1905+1G>A Uncertain significance ★★ same type
- EEF1D p.Arg585Cys Uncertain significance ★★ ⚠ same type
- EEF1D p.Asp100Gly Uncertain significance ★★ same type
- EEF1D p.Asp386Asn Uncertain significance ★★ ⚠ same type
- EEF1D p.Gly351Ala Uncertain significance ★★ same type
- EEF1D p.Pro350Leu Uncertain significance ★★ same type
- EEF1D p.Ser213Asn Uncertain significance ★★ same type
- EEF1D p.Thr575Met 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/eef1d-p-ala99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown