CSF2 p.Gly92=
c.276C>T · rs141989882 · VCV792010
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.572%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -4.4 |
| Overall | ||
| CADD | 1.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.572%
African / African-American · 429/75,056 alleles
Filtering AF
0.527%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.509%
Overall
0.0306%
494/1,613,466 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.572% | 175 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Admixed American | 0.0416% | 2,401 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.00439% | 22,773 |
| European (non-Finnish) | 0.000169% | 590,012 |
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
- CSF2
- Protein
- p.Gly92=
- Coding
- c.276C>T
- MANE Select
- NM_000758
- dbSNP
- rs141989882
- Type
- single nucleotide variant
- Location
- chr5:132074884 (GRCh38)
- Gene constraint
- LOEUF 0.619 · pLI 0.85 (gnomAD)
- Structure
- AlphaFold pLDDT 88.30 · 11 PDB
- Residue 92
- an α-helix; a disulfide bond
Similar variants
- CSF2 p.Thr115Ile Likely benign ★★ same type
- CSF2 p.Ala13Thr Uncertain significance ★ ⚠ same type
- CSF2 p.Arg21Cys Uncertain significance ★ ⚠ same type
- CSF2 p.Arg41His Uncertain significance ★ ⚠ same type
- CSF2 p.Arg84Pro Uncertain significance ★ ⚠ same type
- CSF2 p.Glu52Asp Uncertain significance ★ ⚠ same type
- CSF2 p.Leu127Met Uncertain significance ★ ⚠ same type
- CSF2 p.Met53Thr 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/csf2-p-gly92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown