EBF3 p.Ala39=
c.117C>G · rs553372063 · VCV2640976
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00234%, sas)
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 | GERP 0.93, phastCons 1 |
| Overall | ||
| CADD | 15.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00234%
South Asian · 2/85,576 alleles
Filtering AF
0.000388%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000145%
Overall
0.000134%
2/1,489,330 alleles · very rare
exomes 1/1,339,362 · genomes 1/149,968 · joint denominator
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.Ala39=
- Coding
- c.117C>G
- MANE Select
- NM_001375380
- dbSNP
- rs553372063
- Type
- single nucleotide variant
- Location
- chr10:129963652 (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-ala39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown