EFNB2 p.Thr266=
c.798G>A · rs71640250 · VCV742043
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0183%, amr)
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 -2.8 | GERP -5.8 |
| Overall | ||
| CADD | 6.846 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0183%
Admixed American · 11/60,000 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00785%
Overall
0.00235%
38/1,614,052 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0183% | 5,455 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.00169% | 59,002 |
| African / African-American | 0.00133% | 74,920 |
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
- EFNB2
- Protein
- p.Thr266=
- Coding
- c.798G>A
- MANE Select
- NM_004093
- dbSNP
- rs71640250
- Type
- single nucleotide variant
- Location
- chr13:106493244 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.60 · 10 PDB
Similar variants
- EFNB2 p.Tyr73Ter Likely pathogenic ★ same type
- EFNB2 p.Ala157Thr Uncertain significance ★ ⚠ same type
- EFNB2 p.Ala296Ser Uncertain significance ★ ⚠ same type
- EFNB2 p.Arg156Lys Uncertain significance ★ ⚠ same type
- EFNB2 p.Arg182His Uncertain significance ★ ⚠ same type
- EFNB2 p.Arg253Gln Uncertain significance ★ ⚠ same type
- EFNB2 p.Arg253Trp Uncertain significance ★ ⚠ same type
- EFNB2 p.Arg277Cys 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/efnb2-p-thr266 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown