Is FANCF p.Arg46= (c.138G>A) pathogenic?

FANCF p.Arg46= (c.138G>A) is classified Likely benign in FANCF (ClinVar, Single submitter, 1 submitter; last evaluated 2026-04-01). Absent from gnomAD v4.1.

How common is FANCF p.Arg46= (c.138G>A) in the general population?

FANCF p.Arg46= (c.138G>A) is absent from gnomAD v4.1 (gnomAD).

FANCF p.Arg46=

c.138G>A · VCV4874309

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.23	GERP -0.9
Overall
CADD	6.107	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FANCF
Protein: p.Arg46=
Coding: c.138G>A
MANE Select: NM_022725
Type: single nucleotide variant
Location: chr11:22625673 (GRCh38)
Structure: AlphaFold pLDDT 78.87 · 7 PDB
Residue 46: an α-helix

Full FANCF gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FANCF p.Arg46Gly Uncertain significance ★★ ⚠ same residue
FANCF p.Arg46Gln 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

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-arg46 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown