EAF1 p.Asp206=
c.618C>T · rs34668493 · VCV767886
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.81%, 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 -14 | GERP -4.2 |
| Overall | ||
| CADD | 7.216 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.81%
African / African-American · 1,359/75,012 alleles
Filtering AF
1.73%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.7%
Overall
0.12%
1,941/1,613,952 alleles · low-frequency
exomes 1,077/1,461,690 · genomes 864/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.81% | 55 |
| Middle Eastern | 0.247% | 404 |
| Admixed American | 0.22% | 455 |
| Remaining individualsnot grpmax-eligible | 0.189% | 530 |
| European (non-Finnish) | 0.0255% | 3,920 |
| Finnishnot grpmax-eligible | 0.0141% | 7,114 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,803 |
| South Asian | 0.00549% | 18,214 |
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
- EAF1
- Protein
- p.Asp206=
- Coding
- c.618C>T
- MANE Select
- NM_033083
- dbSNP
- rs34668493
- Type
- single nucleotide variant
- Location
- chr3:15436433 (GRCh38)
- Gene constraint
- LOEUF 1.012 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.79 · 2 PDB
- Residue 206
- the 'disordered' region; the 'necessary for transactivation activity' region
Similar variants
- EAF1 p.Thr133= Benign ★★ same type
- EAF1 p.Ala147Ser Uncertain significance ★ ⚠ same type
- EAF1 p.Arg122Gln Uncertain significance ★ ⚠ same type
- EAF1 p.Arg233Met Uncertain significance ★ ⚠ same type
- EAF1 p.Arg233Thr Uncertain significance ★ ⚠ same type
- EAF1 p.Arg27Gln Uncertain significance ★ ⚠ same type
- EAF1 p.Asn216Ser Uncertain significance ★ ⚠ same type
- EAF1 p.Asn6Ser 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/eaf1-p-asp206 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown