FANCF p.Arg96=
c.288C>A · VCV4911076
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.005 | GERP -3.5, phastCons 0.21 |
| Overall | ||
| CADD | 8.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,046 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,092 alleles · very rare
exomes 0/1,461,846 · genomes 2/152,246 · joint denominator
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
- FANCF
- Protein
- p.Arg96=
- Coding
- c.288C>A
- MANE Select
- NM_022725
- Type
- single nucleotide variant
- Location
- chr11:22625523 (GRCh38)
- Structure
- AlphaFold pLDDT 78.87 · 7 PDB
- Residue 96
- an α-helix
Similar variants
- FANCF p.Gln65Ter Likely pathogenic ★★ same type
- FANCF p.Glu220Ter Pathogenic/Likely pathogenic ★★ same type
- FANCF p.Glu223Ter Pathogenic/Likely pathogenic ★★ same type
- FANCF p.Met1Arg Pathogenic/Likely pathogenic ★★ same type
- FANCF c.-21A>G Uncertain significance ★★ same type
- FANCF c.-31T>C Uncertain significance ★★ same type
- FANCF c.*1879T>C Uncertain significance ★★ same type
- FANCF p.Ala124Ser 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/fancf-p-arg96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown