EOMES p.Glu113=
c.339G>A · rs546902544 · VCV727252
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.435%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -0.4, phastCons 1 |
| Overall | ||
| CADD | 13.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.435%
African / African-American · 286/65,706 alleles
Filtering AF
0.394%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.378%
Overall
0.0213%
302/1,419,972 alleles · rare
exomes 122/1,268,114 · genomes 180/151,858 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.435% | 230 |
| Remaining individualsnot grpmax-eligible | 0.0203% | 4,928 |
| Admixed American | 0.0193% | 5,179 |
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
- EOMES
- Protein
- p.Glu113=
- Coding
- c.339G>A
- MANE Select
- NM_001278182
- dbSNP
- rs546902544
- Type
- single nucleotide variant
- Location
- chr3:27721956 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
Similar variants
- EOMES p.Tyr231Cys Uncertain significance ★★ ⚠ same type
- EOMES p.Pro641= Benign ★★ same type
- EOMES p.Ser392= Likely benign ★★ same type
- EOMES p.Ser91Arg Likely benign ★★ same type
- EOMES p.Ala118Pro Uncertain significance ★ ⚠ same type
- EOMES p.Ala17Pro Uncertain significance ★ ⚠ same type
- EOMES p.Ala206Gly Uncertain significance ★ ⚠ same type
- EOMES p.Ala218Thr 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/eomes-p-glu113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown