Is BACH2 p.Ile579Val (c.1735A>G) pathogenic?

BACH2 p.Ile579Val (c.1735A>G) is classified Likely benign in BACH2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-06). AlphaMissense: likely benign (0.1945); Rare (popmax 0.287%, afr).

How common is BACH2 p.Ile579Val (c.1735A>G) in the general population?

BACH2 p.Ile579Val (c.1735A>G) is rare (popmax 0.287%, afr) (gnomAD).

What do computational predictors say about BACH2 p.Ile579Val (c.1735A>G)?

AlphaMissense predicts likely benign (score 0.1945) — an in-silico prediction, not a clinical call.

BACH2 p.Ile579Val

c.1735A>G · rs145146483 · VCV749763

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1945 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.287%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1945	likely benign
REVEL	0.215	benign-leaning
SaProt	LLR -5.54	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 6.2	GERP 1.3, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 18 kb · p 2.2e-13 · regional, not allelic
Overall
CADD	23.4	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 0.287% African / African-American · 215/75,024 alleles

Filtering AF 0.255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.243%

Overall 0.0163% 263/1,614,148 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.287%	349
Admixed American	0.0283%	3,531
Remaining individualsnot grpmax-eligible	0.0192%	5,209
East Asian	0.00223%	44,866
European (non-Finnish)	0.00153%	65,557

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.Ile579Val
Coding: c.1735A>G
MANE Select: NM_021813
dbSNP: rs145146483
Type: single nucleotide variant
Location: chr6:89950371 (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

Similar variants

BACH2 p.Ala148Val Uncertain significance ★★ ⚠ same type
BACH2 p.Ala205Thr Uncertain significance ★★ ⚠ same type
BACH2 p.Ala304Glu Uncertain significance ★★ ⚠ same type
BACH2 p.Ala479Val Uncertain significance ★★ ⚠ same type
BACH2 p.Ala529Val Uncertain significance ★★ ⚠ same type
BACH2 p.Ala747Val Uncertain significance ★★ ⚠ same type
BACH2 p.Ala756Val Uncertain significance ★★ ⚠ same type
BACH2 p.Ala761Ser 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/bach2-p-ile579val (accessed [today's date]).

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