FCGR2A p.Pro48=
c.144G>A · rs553243113 · VCV3039046
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0692%, sas)
Conditions
1
FCGR2A-related disorder
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 -16 | GERP -3.7 |
| Overall | ||
| CADD | 5.741 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0692%
South Asian · 63/91,084 alleles
Filtering AF
0.0554%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0505%
Overall
0.0215%
347/1,614,164 alleles · ultra-rare
exomes 321/1,461,894 · genomes 26/152,270 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0692% | 1,446 |
| Finnishnot grpmax-eligible | 0.0609% | 1,642 |
| European (non-Finnish) | 0.0197% | 5,065 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,813 |
| Admixed American | 0.005% | 20,005 |
| African / African-American | 0.00133% | 75,038 |
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.Pro48=
- Coding
- c.144G>A
- MANE Select
- NM_001136219
- dbSNP
- rs553243113
- Type
- single nucleotide variant
- Location
- chr1:161506371 (GRCh38)
- Gene constraint
- LOEUF 0.922 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.04 · 10 PDB
- Residue 48
- the ig-like c2-type 1 domain
Disease context
FCGR2A-related disorder
Similar variants
- FCGR2A p.Asn51= Likely benign same condition
- 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-pro48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown