FCGR2A p.Pro293=
c.879C>T · rs12029217 · VCV402855
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 22.8%, eas) — too common for a highly-penetrant pathogenic allele
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 -0.39 | GERP -1.2 |
| Overall | ||
| CADD | 1.774 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
22.8%
East Asian · 10,134/44,484 alleles
Filtering AF
22.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.3%
Overall
10.6%
171,166/1,609,480 alleles · common
exomes 157,658/1,457,880 · genomes 13,508/151,600 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 22.8% | 4 |
| Amishnot grpmax-eligible | 20.9% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 13.9% | 7 |
| Remaining individualsnot grpmax-eligible | 11.3% | 9 |
| Admixed American | 11% | 9 |
| European (non-Finnish) | 10.8% | 9 |
| Middle Eastern | 10.6% | 9 |
| South Asian | 9.01% | 11 |
| Finnishnot grpmax-eligible | 6.61% | 15 |
| African / African-American | 3.28% | 31 |
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
- FCGR2A
- Protein
- p.Pro293=
- Coding
- c.879C>T
- MANE Select
- NM_001136219
- dbSNP
- rs12029217
- Type
- single nucleotide variant
- Location
- chr1:161518073 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.04 · 10 PDB
- Residue 293
- the 'disordered' region
Similar variants
- FCGR2A p.Pro293Ala Uncertain significance ★ ⚠ same residue
- FCGR2A c.780+1G>A Uncertain significance ★★ same type
- FCGR2A p.Ser315Gly Uncertain significance ★★ ⚠ same type
- FCGR2A c.365-11G>A Benign ★★ same type
- FCGR2A p.Gln63Arg Benign ★★ same type
- FCGR2A p.Gln63Ter Benign ★★ same type
- FCGR2A p.His167Arg Benign ★★ same type
- FCGR2A p.Pro215= Benign ★★ 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/fcgr2a-p-pro293 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown