EOMES p.Ser392=
c.1176C>T · rs147676215 · VCV771851
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.14%, mid)
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 2.3 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 8.804 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.14%
Middle Eastern · 69/6,058 alleles
Filtering AF
0.923%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.844%
Overall
0.0565%
911/1,612,780 alleles · low-frequency
exomes 813/1,460,536 · genomes 98/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.14% | 88 |
| Admixed American | 0.113% | 882 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0947% | 1,056 |
| Remaining individualsnot grpmax-eligible | 0.0945% | 1,059 |
| South Asian | 0.089% | 1,124 |
| European (non-Finnish) | 0.0495% | 2,019 |
| African / African-American | 0.0293% | 3,408 |
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.Ser392=
- Coding
- c.1176C>T
- MANE Select
- NM_001278182
- dbSNP
- rs147676215
- Type
- single nucleotide variant
- Location
- chr3:27718876 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 56.74
- Residue 392
- a DNA-binding region
Similar variants
- EOMES p.Tyr231Cys Uncertain significance ★★ ⚠ same type
- EOMES p.Glu113= Likely benign ★★ same type
- EOMES p.Pro641= 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-ser392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown