Is BATF3 p.Ala17Val (c.50C>T) pathogenic?

BATF3 p.Ala17Val (c.50C>T) is classified Uncertain significance in BATF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-07). AlphaMissense: likely benign (0.2506); Very rare (popmax 0.00889%, amr).

How common is BATF3 p.Ala17Val (c.50C>T) in the general population?

BATF3 p.Ala17Val (c.50C>T) is very rare (popmax 0.00889%, amr) (gnomAD).

What do computational predictors say about BATF3 p.Ala17Val (c.50C>T)?

AlphaMissense predicts likely benign (score 0.2506) — an in-silico prediction, not a clinical call.

BATF3 p.Ala17Val

c.50C>T · rs1313324995 · VCV2534888

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2506 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00889%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2506	likely benign
REVEL	0.058	moderately benign-leaning
SaProt	LLR -6.90	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 1.5	GERP 0.49, phastCons 0.12
Regional constraint	o/e 0.83	unconstrained · MANE · 13 kb · p 0.03 · regional, not allelic
Overall
CADD	18.27	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 0.00889% Admixed American · 3/33,762 alleles

Filtering AF 0.00235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00125%

Overall 0.000222% 3/1,348,468 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: BATF3
Protein: p.Ala17Val
Coding: c.50C>T
MANE Select: NM_018664
dbSNP: rs1313324995
Type: single nucleotide variant
Location: chr1:212699713 (GRCh38)
Gene constraint: LOEUF 1.094 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 83.05
Residue 17: the 'disordered' region

Full BATF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BATF3 p.Asp119Gly Uncertain significance ★ ⚠ same type
BATF3 p.Asp34Val Uncertain significance ★ ⚠ same type
BATF3 p.Gln72Arg Uncertain significance ★ ⚠ same type
BATF3 p.Gly123Ser Uncertain significance ★ ⚠ same type
BATF3 p.Gly4Arg Uncertain significance ★ ⚠ same type
BATF3 p.Leu5Phe Uncertain significance ★ ⚠ same type
BATF3 p.Lys62Glu Uncertain significance ★ ⚠ same type
BATF3 p.Ser2Trp 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/batf3-p-ala17val (accessed [today's date]).

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