IRF2BPL p.Phe30=
c.90C>T · rs371546648 · VCV3026140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0255%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.7 | GERP -0.93, phastCons 1 |
| Overall | ||
| CADD | 11.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0255%
African / African-American · 19/74,454 alleles
Filtering AF
0.0167%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0138%
Overall
0.0018%
29/1,610,152 alleles · ultra-rare
exomes 15/1,458,032 · genomes 14/152,120 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0255% | 3,919 |
| Admixed American | 0.00167% | 59,868 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,326 |
| European (non-Finnish) | 0.000679% | 147,346 |
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
- IRF2BPL
- Protein
- p.Phe30=
- Coding
- c.90C>T
- MANE Select
- NM_024496
- dbSNP
- rs371546648
- Type
- single nucleotide variant
- Location
- chr14:77027703 (GRCh38)
- Gene constraint
- LOEUF 0.544 · pLI 0.91 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.01 · 1 PDB
Similar variants
- IRF2BPL p.Phe30Ser Uncertain significance ★ ⚠ same residue
- IRF2BPL p.Arg188Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln117Ter Likely pathogenic ★★ same type
- IRF2BPL p.Gln119Ter Likely pathogenic ★★ same type
- IRF2BPL p.Gln120Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln121Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln122Ter Pathogenic/Likely pathogenic ★★ same type
- IRF2BPL p.Gln167Ter 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/irf2bpl-p-phe30 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown