EBF3 p.Ala411=
c.1233G>A · VCV3274350
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Conditions
1
Inborn genetic diseases
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 -7.9 | GERP -5.2 |
| Overall | ||
| CADD | 1.284 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,842 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00106%
17/1,610,994 alleles · very rare
exomes 16/1,458,824 · genomes 1/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,711 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,350 |
| European (non-Finnish) | 0.00102% | 98,204 |
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.Ala411=
- Coding
- c.1233G>A
- MANE Select
- NM_001375380
- Type
- single nucleotide variant
- Location
- chr10:129842255 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 411
- an α-helix
Similar variants
- EBF3 p.Arg152Gly Pathogenic ★★ same condition
- EBF3 p.Arg163Gln Pathogenic ★★ same condition
- EBF3 p.Arg209Gln Pathogenic/Likely pathogenic ★★ same condition
- EBF3 c.*9A>G Uncertain significance ★★ ⚠ same condition
- EBF3 p.Asn100Asp Uncertain significance ★★ ⚠ same condition
- EBF3 p.Asp286Asn Uncertain significance ★★ ⚠ same condition
- EBF3 p.Gly291Arg Uncertain significance ★★ ⚠ same condition
- EBF3 p.Thr33Ala Benign/Likely benign ★★ same condition
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-ala411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown