FANCF p.Ala16=
c.48G>C · VCV4911080
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -13 | GERP -3.4 |
| Overall | ||
| CADD | 0.885 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,090 alleles
Overall
6.84e-05%
1/1,461,854 alleles · very rare
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.Ala16=
- Coding
- c.48G>C
- MANE Select
- NM_022725
- Type
- single nucleotide variant
- Location
- chr11:22625763 (GRCh38)
- Structure
- AlphaFold pLDDT 78.87 · 7 PDB
- Residue 16
- an α-helix
Similar variants
- FANCF p.Ala16Val Uncertain significance ★ ⚠ same residue
- 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
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-ala16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown