CSF1R p.Ser947=
c.2841T>C · rs148054244 · VCV714283
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, 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 -0.68 | GERP -3.9 |
| Overall | ||
| CADD | 0.797 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
African / African-American · 895/75,038 alleles
Filtering AF
1.13%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1%
Overall
0.0592%
955/1,613,798 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.19% | 84 |
| Middle Eastern | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0416% | 2,403 |
| Admixed American | 0.0367% | 2,726 |
| European (non-Finnish) | 0.000763% | 131,100 |
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
- CSF1R
- Protein
- p.Ser947=
- Coding
- c.2841T>C
- MANE Select
- NM_001288705
- dbSNP
- rs148054244
- Type
- single nucleotide variant
- Location
- chr5:150054147 (GRCh38)
- Gene constraint
- LOEUF 0.485 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 78.08 · 26 PDB
- Residue 947
- the 'disordered' region; a UniProt-annotated variant site (in banddos)
Similar variants
- CSF1R p.Ser947Cys Uncertain significance ★ ⚠ same residue
- CSF1R p.Ser947Pro Uncertain significance ★ ⚠ same residue
- CSF1R p.Ala780Val Likely pathogenic ★★ same type
- CSF1R p.Ala781Val Pathogenic ★★ same type
- CSF1R p.Arg676Ter Pathogenic ★★ same type
- CSF1R p.Arg777Gln Pathogenic ★★ same type
- CSF1R p.Arg777Trp Pathogenic/Likely pathogenic ★★ same type
- CSF1R p.Arg782Cys Pathogenic/Likely pathogenic ★★ 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/csf1r-p-ser947 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown