Is APOBEC3F p.Ser28Phe (c.83C>T) pathogenic?

APOBEC3F p.Ser28Phe (c.83C>T) is classified Uncertain significance in APOBEC3F (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-04). AlphaMissense: ambiguous (0.4384); Absent from gnomAD v4.1.

How common is APOBEC3F p.Ser28Phe (c.83C>T) in the general population?

APOBEC3F p.Ser28Phe (c.83C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about APOBEC3F p.Ser28Phe (c.83C>T)?

AlphaMissense predicts ambiguous (score 0.4384) — an in-silico prediction, not a clinical call.

APOBEC3F p.Ser28Phe

c.83C>T · VCV4126444

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4384 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4384	ambiguous
REVEL	0.122	moderately benign-leaning
SaProt	LLR -5.75	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -1.1
Regional constraint	o/e 0.97	unconstrained · MANE · 12 kb · p 0.49 · regional, not allelic
Overall
CADD	0.187	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: APOBEC3F
Protein: p.Ser28Phe
Coding: c.83C>T
MANE Select: NM_145298
Type: single nucleotide variant
Location: chr22:39043002 (GRCh38)
Gene constraint: LOEUF 1.014 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.31 · 10 PDB

Full APOBEC3F gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

APOBEC3F p.Asn346Ser Benign/Likely benign ★★ same type
APOBEC3F p.Glu151Asp Likely benign ★★ same type
APOBEC3F p.Glu373Lys Likely benign ★★ same type
APOBEC3F p.Pro191= Benign ★★ same type
APOBEC3F p.Tyr307Cys Benign ★★ ⚠ same type
APOBEC3F c.196G>C Uncertain significance ★ ⚠ same type
APOBEC3F p.Arg128Lys Uncertain significance ★ ⚠ same type
APOBEC3F p.Arg143His 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/apobec3f-p-ser28phe (accessed [today's date]).

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