Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.41%, eas)
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 3.5 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 9.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.41%
East Asian · 1,083/44,882 alleles
Filtering AF
2.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.25%
Overall
0.186%
2,996/1,614,090 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.41% | 41 |
| African / African-American | 1.24% | 80 |
| Middle Eastern | 0.858% | 117 |
| Remaining individualsnot grpmax-eligible | 0.237% | 422 |
| Finnishnot grpmax-eligible | 0.231% | 432 |
| South Asian | 0.192% | 521 |
| Admixed American | 0.143% | 698 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0507% | 1,974 |
| European (non-Finnish) | 0.0302% | 3,315 |
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
- EEF2
- Protein
- p.Ile556=
- Coding
- c.1668C>A
- MANE Select
- NM_001961
- dbSNP
- rs2305111
- Type
- single nucleotide variant
- Location
- chr19:3979374 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.97 · 26 PDB
- Residue 556
- an α-helix
Similar variants
- EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala338Gly Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala624Thr Uncertain significance ★★ ⚠ same type
- EEF2 p.Ala808Val Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg633His Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg647His Uncertain significance ★★ ⚠ same type
- EEF2 p.Arg726Trp 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/eef2-p-ile556 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown