CSF2RB p.Pro82=
c.246C>G · rs200960215 · VCV1573849
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.388%, eas)
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 -0.011 | GERP -0.64 |
| Overall | ||
| CADD | 3.465 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.388%
East Asian · 174/44,886 alleles
Filtering AF
0.341%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.323%
Overall
0.0139%
225/1,614,210 alleles · rare
exomes 217/1,461,880 · genomes 8/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.388% | 258 |
| South Asian | 0.0351% | 2,846 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,465 |
| Admixed American | 0.005% | 20,007 |
| Finnishnot grpmax-eligible | 0.00156% | 64,038 |
| European (non-Finnish) | 8.47e-05% | 1,180,040 |
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
- CSF2RB
- Protein
- p.Pro82=
- Coding
- c.246C>G
- MANE Select
- NM_000395
- dbSNP
- rs200960215
- Type
- single nucleotide variant
- Location
- chr22:36926032 (GRCh38)
- Gene constraint
- LOEUF 0.511 · pLI 0.93 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.50 · 10 PDB
Similar variants
- CSF2RB p.Ala185Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala255Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala314Val Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala394Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala455Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala576Thr Uncertain significance ★★ ⚠ same type
- CSF2RB p.Ala662Thr 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/csf2rb-p-pro82 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown