Is BATF2 p.Arg33Gln (c.98G>A) pathogenic?

BATF2 p.Arg33Gln (c.98G>A) is classified Uncertain significance in BATF2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-10). AlphaMissense: ambiguous (0.4066); Very rare (popmax 0.00337%, sas).

How common is BATF2 p.Arg33Gln (c.98G>A) in the general population?

BATF2 p.Arg33Gln (c.98G>A) is very rare (popmax 0.00337%, sas) (gnomAD).

What do computational predictors say about BATF2 p.Arg33Gln (c.98G>A)?

AlphaMissense predicts ambiguous (score 0.4066) — an in-silico prediction, not a clinical call.

BATF2 p.Arg33Gln

c.98G>A · VCV3479785

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4066 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00337%, sas)

Computational evidence

Protein change
AlphaMissense	0.4066	ambiguous
REVEL	0.341	indeterminate
SaProt	LLR -9.79	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 0.72, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 7,782 bp · p 0.014 · regional, not allelic
Overall
CADD	28.9	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 0.00337% South Asian · 3/89,038 alleles

Filtering AF 0.000895% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000448%

Overall 0.000686% 11/1,602,766 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00337%	29,679
Remaining individualsnot grpmax-eligible	0.00322%	31,042
Admixed American	0.00172%	58,090
European (non-Finnish)	0.000426%	234,954

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.Arg33Gln
Coding: c.98G>A
MANE Select: NM_138456
Type: single nucleotide variant
Location: chr11:64994491 (GRCh38)
Gene constraint: LOEUF 1.522 · pLI 0.03 (gnomAD)
Structure: AlphaFold pLDDT 62.92
Residue 33: 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 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.Arg28Gln Uncertain significance ★ ⚠ same type
BATF2 p.Arg28Trp 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-arg33gln (accessed [today's date]).

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