EBF3 p.Thr280=
c.840C>T · rs61729248 · VCV715911
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0208%, nfe)
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 -4 | GERP -3.7 |
| Overall | ||
| CADD | 6.917 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0208%
European (non-Finnish) · 246/1,180,050 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0179%
Overall
0.016%
259/1,614,110 alleles · ultra-rare
exomes 240/1,461,882 · genomes 19/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0208% | 4,797 |
| Admixed American | 0.00833% | 12,003 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| African / African-American | 0.004% | 24,979 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
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.Thr280=
- Coding
- c.840C>T
- MANE Select
- NM_001375380
- dbSNP
- rs61729248
- Type
- single nucleotide variant
- Location
- chr10:129867854 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 280
- the ipt/tig domain; a β-strand
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-thr280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown