EOMES p.Ala120=
c.360C>T · rs916686138 · VCV3049265
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0523%, nfe)
Conditions
1
EOMES-related disorder
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 -2.7 |
| Overall | ||
| CADD | 6.812 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0523%
European (non-Finnish) · 562/1,073,662 alleles
Filtering AF
0.0487%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0473%
Overall
0.0423%
580/1,370,354 alleles · ultra-rare
exomes 552/1,230,252 · genomes 28/140,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0523% | 1,910 |
| Remaining individualsnot grpmax-eligible | 0.0172% | 5,802 |
| African / African-American | 0.0111% | 9,039 |
| East Asian | 0.00322% | 31,048 |
| Finnishnot grpmax-eligible | 0.00192% | 52,090 |
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.Ala120=
- Coding
- c.360C>T
- MANE Select
- NM_001278182
- dbSNP
- rs916686138
- Type
- single nucleotide variant
- Location
- chr3:27721935 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
- Residue 120
- a UniProt-annotated variant site (in)
Disease context
EOMES-related disorder
Similar variants
- EOMES p.Ala123= Likely benign same condition
- EOMES p.Ala125= Likely benign same condition
- EOMES p.Ala33= Likely benign same condition
- EOMES p.Pro203= Likely benign same condition
- EOMES p.Ala130del Likely benign same condition
- EOMES p.Tyr231Cys Uncertain significance ★★ ⚠ same type
- EOMES p.Glu113= Likely benign ★★ same type
- EOMES p.Pro641= Benign ★★ 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-ala120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown