Is BATF2 p.Arg28Gln (c.83G>A) pathogenic?

BATF2 p.Arg28Gln (c.83G>A) is classified Uncertain significance in BATF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-28). AlphaMissense: ambiguous (0.4397); Very rare (popmax 0.00134%, afr).

How common is BATF2 p.Arg28Gln (c.83G>A) in the general population?

BATF2 p.Arg28Gln (c.83G>A) is very rare (popmax 0.00134%, afr) (gnomAD).

What do computational predictors say about BATF2 p.Arg28Gln (c.83G>A)?

AlphaMissense predicts ambiguous (score 0.4397) — an in-silico prediction, not a clinical call.

BATF2 p.Arg28Gln

c.83G>A · rs780112822 · VCV2594524

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4397 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Computational evidence

Protein change
AlphaMissense	0.4397	ambiguous
REVEL	0.329	indeterminate
SaProt	LLR -10.54	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP 0.72, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 7,782 bp · p 0.014 · regional, not allelic
Overall
CADD	24.0	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

Grpmax group 0.00134% African / African-American · 1/74,770 alleles

Filtering AF 0.000502% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000367%

Overall 0.000873% 14/1,604,244 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.00158%	63,274
African / African-Americangrpmax	0.00134%	74,770
South Asian	0.00112%	89,316
European (non-Finnish)	0.000936%	106,867

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: BATF2
Protein: p.Arg28Gln
Coding: c.83G>A
MANE Select: NM_138456
dbSNP: rs780112822
Type: single nucleotide variant
Location: chr11:64994506 (GRCh38)
Gene constraint: LOEUF 1.522 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.92
Residue 28: the bzip domain; the 'disordered' region; the 'basic motif' region

Full BATF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BATF2 p.Arg28Trp Uncertain significance ★ ⚠ same residue
BATF2 c.40-2A>T Uncertain significance ★ same type
BATF2 p.Ala178Asp Uncertain significance ★ ⚠ same type
BATF2 p.Ala29Val Uncertain significance ★ ⚠ same type
BATF2 p.Ala31Thr Uncertain significance ★ ⚠ same type
BATF2 p.Arg33Gln Uncertain significance ★ ⚠ same type
BATF2 p.Arg75Trp Uncertain significance ★ ⚠ same type
BATF2 p.Arg82His 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/batf2-p-arg28gln (accessed [today's date]).

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