Is FANCF c.*287C>T pathogenic?

FANCF c.287C>T is classified Uncertain significance in FANCF (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Very rare (popmax 0.00998%, sas); Associated with Fanconi anemia complementation group F.

What condition is associated with FANCF c.*287C>T?

FANCF c.*287C>T is associated with Fanconi anemia complementation group F (ClinVar).

How common is FANCF c.*287C>T in the general population?

FANCF c.*287C>T is very rare (popmax 0.00998%, sas) (gnomAD).

FANCF c.*287C>T

rs886048156 · VCV304196

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00998%, sas)

Conditions

Fanconi anemia complementation group F

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 0.12	GERP -1.4
Non-coding constraint	Z -0.65	1 kb window · o/e 1.06 · regional · uncalibrated
Overall
CADD	1.873	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00998% South Asian · 4/40,100 alleles

Filtering AF 0.00332% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00197%

Overall 0.00127% 6/471,610 alleles · very rare exomes 6/319,364 · genomes 0/152,246 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00998%	10,025
Remaining individualsnot grpmax-eligible	0.00941%	10,629

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
Coding: c.*287C>T
MANE Select: NM_022725
dbSNP: rs886048156
Type: single nucleotide variant
Location: chr11:22624399 (GRCh38)
Structure: AlphaFold pLDDT 78.87 · 7 PDB

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

Disease context

Fanconi anemia complementation group F — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FANCF p.Gln65Ter Likely pathogenic ★★ same condition
FANCF p.Glu220Ter Pathogenic/Likely pathogenic ★★ same condition
FANCF p.Met1Arg Pathogenic/Likely pathogenic ★★ same condition
FANCF c.-21A>G Uncertain significance ★★ same condition
FANCF c.-31T>C Uncertain significance ★★ same condition
FANCF c.*1879T>C Uncertain significance ★★ same condition
FANCF p.Ala124Ser Uncertain significance ★★ ⚠ same condition
FANCF p.Ala206Val Uncertain significance ★★ ⚠ 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/fancf-c-star-287c-t (accessed [today's date]).

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