EBF3 p.Ala406=
c.1218G>A · rs144257779 · VCV3044256
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0348%, afr)
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 -8.4 | GERP -5.2 |
| Overall | ||
| CADD | 0.823 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0348%
African / African-American · 26/74,670 alleles
Filtering AF
0.0243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0209%
Overall
0.00399%
64/1,603,980 alleles · ultra-rare
exomes 50/1,451,900 · genomes 14/152,080 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0348% | 2,872 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,019 |
| European (non-Finnish) | 0.00298% | 33,560 |
| South Asian | 0.00112% | 89,484 |
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
- EBF3
- Protein
- p.Ala406=
- Coding
- c.1218G>A
- MANE Select
- NM_001375380
- dbSNP
- rs144257779
- Type
- single nucleotide variant
- Location
- chr10:129842270 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 406
- an α-helix
Similar variants
- EBF3 c.486-1G>A Pathogenic ★★ same type
- EBF3 c.555-2A>G Likely pathogenic ★★ same type
- EBF3 p.Arg152Gly Pathogenic ★★ same type
- EBF3 p.Arg163Gln Pathogenic ★★ same type
- EBF3 p.Arg163Leu Pathogenic ★★ same type
- EBF3 p.Arg163Trp Pathogenic/Likely pathogenic ★★ same type
- EBF3 p.Arg206Ter Pathogenic ★★ same type
- EBF3 p.Arg209Gln Pathogenic/Likely pathogenic ★★ 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/ebf3-p-ala406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown