Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0304%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.331 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.5 | GERP -5.7 |
| Overall | ||
| CADD | 5.425 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0304%
South Asian · 26/85,634 alleles
Filtering AF
0.0213%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0182%
Overall
0.00843%
129/1,530,460 alleles · ultra-rare
exomes 119/1,379,544 · genomes 10/150,916 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0304% | 3,294 |
| Remaining individualsnot grpmax-eligible | 0.0121% | 8,231 |
| African / African-American | 0.00962% | 10,391 |
| European (non-Finnish) | 0.00751% | 13,322 |
| Admixed American | 0.00561% | 17,833 |
| Finnishnot grpmax-eligible | 0.00183% | 54,668 |
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.Asn581=
- Coding
- c.1743C>T
- MANE Select
- NM_001375380
- dbSNP
- rs7092828
- Type
- single nucleotide variant
- Location
- chr10:129840261 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
Similar variants
- EBF3 p.Asn581fs Uncertain significance ★ same residue
- 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
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-asn581 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown