EBF4 p.Arg164=
c.492G>T · rs61733881 · VCV783857
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.32%, 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 0.4 | phastCons 0.98 |
| Overall | ||
| CADD | 7.051 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.32%
African / African-American · 970/73,280 alleles
Filtering AF
1.25%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.23%
Overall
0.0718%
1,115/1,553,394 alleles · low-frequency
exomes 510/1,401,118 · genomes 605/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.32% | 76 |
| Admixed American | 0.134% | 749 |
| Remaining individualsnot grpmax-eligible | 0.093% | 1,075 |
| Middle Eastern | 0.0502% | 1,993 |
| South Asian | 0.00356% | 28,069 |
| European (non-Finnish) | 0.00122% | 81,981 |
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
- EBF4
- Protein
- p.Arg164=
- Coding
- c.492G>T
- MANE Select
- NM_001395167
- dbSNP
- rs61733881
- Type
- single nucleotide variant
- Location
- chr20:2709577 (GRCh38)
- Gene constraint
- LOEUF 0.868 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.60
- Residue 164
- a functional site (interaction with dna)
Similar variants
- EBF4 p.Ile91= Benign ★★ same type
- EBF4 p.Ala102Thr Uncertain significance ★ ⚠ same type
- EBF4 p.Ala102Val Uncertain significance ★ ⚠ same type
- EBF4 p.Ala402Thr Uncertain significance ★ ⚠ same type
- EBF4 p.Ala40Thr Uncertain significance ★ ⚠ same type
- EBF4 p.Ala438Ser Uncertain significance ★ ⚠ same type
- EBF4 p.Ala522Val Uncertain significance ★ ⚠ same type
- EBF4 p.Ala557Val 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/ebf4-p-arg164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown