FANCC p.Phe14=
c.42T>C · rs760653185 · VCV824771
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP -0.63, phastCons 1 |
| Overall | ||
| CADD | 9.903 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,026 alleles
Overall
6.19e-05%
1/1,614,228 alleles · very rare
exomes 1/1,461,856 · genomes 0/152,372 · 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
- FANCC
- Protein
- p.Phe14=
- Coding
- c.42T>C
- MANE Select
- NM_000136
- dbSNP
- rs760653185
- Type
- single nucleotide variant
- Location
- chr9:95249250 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.39 · 6 PDB
- Residue 14
- an α-helix
Similar variants
- FANCC c.1073-1G>C Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.1155-1G>C Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.165+1G>T Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.166-2A>G Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.251-2A>C Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.345+1G>A Likely pathogenic ★★ same condition
- FANCC c.346-1G>A Pathogenic/Likely pathogenic ★★ same condition
- FANCC c.456+4A>T Pathogenic ★★ same condition
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/fancc-p-phe14 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown