CSF3 p.Phe170=
c.510C>T · rs774912212 · VCV712650
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.238%, amr)
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 1.9 | GERP -0.84, phastCons 0.96 |
| Overall | ||
| CADD | 7.939 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.238%
Admixed American · 143/59,992 alleles
Filtering AF
0.207%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.194%
Overall
0.00911%
147/1,613,392 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.238% | 420 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,801 |
| European (non-Finnish) | 8.47e-05% | 1,180,025 |
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
- CSF3
- Protein
- p.Phe170=
- Coding
- c.510C>T
- MANE Select
- NM_172219
- dbSNP
- rs774912212
- Type
- single nucleotide variant
- Location
- chr17:40016854 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.67 · 7 PDB
- Residue 170
- an α-helix
Similar variants
- CSF3 p.Ala171Thr Benign ★★ same type
- CSF3 p.Leu154Met Benign ★★ ⚠ same type
- CSF3 p.Pro168= Benign ★★ same type
- CSF3 p.Ala23Thr Uncertain significance ★ ⚠ same type
- CSF3 p.Ala59Thr Uncertain significance ★ ⚠ same type
- CSF3 p.Ala5Val Uncertain significance ★ ⚠ same type
- CSF3 p.Glu123Val Uncertain significance ★ ⚠ same type
- CSF3 p.His73Gln 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/csf3-p-phe170 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown