Is AFF3 p.Leu14Phe (c.40C>T) pathogenic?

AFF3 p.Leu14Phe (c.40C>T) is classified Uncertain significance in AFF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-28). AlphaMissense: likely benign (0.3158); Very rare (popmax 0.000101%, nfe).

How common is AFF3 p.Leu14Phe (c.40C>T) in the general population?

AFF3 p.Leu14Phe (c.40C>T) is very rare (popmax 0.000101%, nfe) (gnomAD).

What do computational predictors say about AFF3 p.Leu14Phe (c.40C>T)?

AlphaMissense predicts likely benign (score 0.3158) — an in-silico prediction, not a clinical call.

AFF3 p.Leu14Phe

c.40C>T · VCV4689123

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3158 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000101%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.3158	likely benign
REVEL	0.207	benign-leaning
SaProt	LLR -7.00	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.3	GERP 0.8, phastCons 1
Regional constraint	o/e 0.26	constrained · MANE · 96 kb · p 0.0011 · regional, not allelic
Overall
CADD	26.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000101% European (non-Finnish) · 1/988,508 alleles

Overall 8.82e-05% 1/1,133,366 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: AFF3
Protein: p.Leu14Phe
Coding: c.40C>T
MANE Select: NM_001386135
Type: single nucleotide variant
Location: chr2:100104415 (GRCh38)
Gene constraint: LOEUF 0.318 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 52.20

Full AFF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AFF3 p.Ala233Thr Pathogenic ★★ ⚠ same type
AFF3 p.Ala233Val Pathogenic/Likely pathogenic ★★ ⚠ same type
AFF3 p.Ile1147Asn Uncertain significance ★★ ⚠ same type
AFF3 p.Leu370Phe Uncertain significance ★★ ⚠ same type
AFF3 p.Pro321Leu Uncertain significance ★★ ⚠ same type
AFF3 p.Ser222Thr Uncertain significance ★★ ⚠ same type
AFF3 p.Thr950Met Uncertain significance ★★ ⚠ same type
AFF3 c.1371+7G>A Likely benign ★★ 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/aff3-p-leu14phe (accessed [today's date]).

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