EBF3 p.Arg77=
c.229A>C · rs75074888 · VCV1222295
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 14.4%, sas) — too common for a highly-penetrant pathogenic allele
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 0.82 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 11.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
14.4%
South Asian · 12,788/88,510 alleles
Filtering AF
14.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 14.2%
Overall
3.63%
57,776/1,591,578 alleles · common
exomes 52,045/1,439,474 · genomes 5,731/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 14.4% | 7 |
| East Asian | 12.9% | 8 |
| Admixed American | 11.7% | 9 |
| Ashkenazi Jewishnot grpmax-eligible | 8.53% | 12 |
| Middle Eastern | 8.32% | 12 |
| Finnishnot grpmax-eligible | 5.71% | 18 |
| Remaining individualsnot grpmax-eligible | 4.27% | 23 |
| European (non-Finnish) | 1.93% | 52 |
| African / African-American | 1.38% | 73 |
| Amishnot grpmax-eligible | 0.877% | 114 |
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.Arg77=
- Coding
- c.229A>C
- MANE Select
- NM_001375380
- dbSNP
- rs75074888
- Type
- single nucleotide variant
- Location
- chr10:129963429 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
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-arg77 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown