IREB2 p.Phe26=
c.78C>T · rs150473761 · VCV2051030
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.788%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 16.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.788%
African / African-American · 588/74,604 alleles
Filtering AF
0.735%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.714%
Overall
0.0437%
700/1,602,728 alleles · rare
exomes 318/1,450,530 · genomes 382/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.788% | 127 |
| Admixed American | 0.112% | 895 |
| Remaining individualsnot grpmax-eligible | 0.0531% | 1,882 |
| Middle Eastern | 0.0165% | 6,056 |
| South Asian | 0.00788% | 12,697 |
| European (non-Finnish) | 0.000426% | 234,638 |
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
- IREB2
- Protein
- p.Phe26=
- Coding
- c.78C>T
- MANE Select
- NM_004136
- dbSNP
- rs150473761
- Type
- single nucleotide variant
- Location
- chr15:78439853 (GRCh38)
- Gene constraint
- LOEUF 0.389 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.11 · 1 PDB
- Residue 26
- a β-strand
Similar variants
- IREB2 p.Ala534Thr Uncertain significance ★★ ⚠ same type
- IREB2 p.Arg697Trp Uncertain significance ★★ ⚠ same type
- IREB2 p.Asn925Thr Uncertain significance ★★ ⚠ same type
- IREB2 p.Cys53Tyr Uncertain significance ★★ same type
- IREB2 p.Glu917Lys Uncertain significance ★★ ⚠ same type
- IREB2 p.Gly184Asp Uncertain significance ★★ ⚠ same type
- IREB2 p.Gly656Ser Uncertain significance ★★ ⚠ same type
- IREB2 p.His22Leu 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/ireb2-p-phe26 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown