Is BACH2 p.Glu5= (c.15G>A) pathogenic?

BACH2 p.Glu5= (c.15G>A) is classified Benign/Likely benign in BACH2 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-01-27). Rare (popmax 0.483%, nfe); Associated with immunodeficiency 60.

What condition is associated with BACH2 p.Glu5= (c.15G>A)?

BACH2 p.Glu5= (c.15G>A) is associated with immunodeficiency 60 (ClinVar).

How common is BACH2 p.Glu5= (c.15G>A) in the general population?

BACH2 p.Glu5= (c.15G>A) is rare (popmax 0.483%, nfe) (gnomAD).

BACH2 p.Glu5=

c.15G>A · rs45447599 · VCV778006

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

rare (popmax 0.483%, nfe)

Conditions

immunodeficiency 60

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.4, phastCons 1
Overall
CADD	12.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.483% European (non-Finnish) · 5,697/1,180,004 alleles

Filtering AF 0.472% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.468%

Overall 0.389% 6,279/1,614,030 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.483%	207
Remaining individualsnot grpmax-eligible	0.346%	289
Middle Eastern	0.33%	303
Admixed American	0.285%	351
Ashkenazi Jewishnot grpmax-eligible	0.223%	449
African / African-American	0.076%	1,316
Finnishnot grpmax-eligible	0.0703%	1,422
South Asian	0.00769%	13,010

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: BACH2
Protein: p.Glu5=
Coding: c.15G>A
MANE Select: NM_021813
dbSNP: rs45447599
Type: single nucleotide variant
Location: chr6:90008830 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.66 · 2 PDB

Full BACH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency 60 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BACH2 p.Ala148Val Uncertain significance ★★ ⚠ same condition
BACH2 p.Ala756Val Uncertain significance ★★ ⚠ same condition
BACH2 p.Asp34Asn Uncertain significance ★★ ⚠ same condition
BACH2 p.Gln378His Uncertain significance ★★ ⚠ same condition
BACH2 p.Gln578Lys Uncertain significance ★★ ⚠ same condition
BACH2 p.Glu788Lys Uncertain significance ★★ ⚠ same condition
BACH2 p.Pro152Leu Uncertain significance ★★ ⚠ same condition
BACH2 p.Pro368Ser Uncertain significance ★★ ⚠ same condition

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/bach2-p-glu5 (accessed [today's date]).

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