Is BAZ2B p.Ala840= (c.2520A>C) pathogenic?

BAZ2B p.Ala840= (c.2520A>C) is classified Benign in BAZ2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-03-04). Common (popmax 13.1%, eas) — too common for a highly-penetrant pathogenic allele; Associated with BAZ2B-related disorder.

What condition is associated with BAZ2B p.Ala840= (c.2520A>C)?

BAZ2B p.Ala840= (c.2520A>C) is associated with BAZ2B-related disorder (ClinVar).

BAZ2B p.Ala840=

Q: How common is BAZ2B p.Ala840= (c.2520A>C) in the general population?

BAZ2B p.Ala840= (c.2520A>C) is common (popmax 13.1%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.2520A>C · rs3755433 · VCV3059173

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 13.1%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

BAZ2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.036	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -0.83, phastCons 1
Overall
CADD	9.047	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 13.1% East Asian · 5,885/44,844 alleles

Filtering AF 12.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 12.7%

Overall 1.7% 27,501/1,614,082 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	13.1%	8
Ashkenazi Jewishnot grpmax-eligible	2.94%	34
South Asian	2.56%	39
Finnishnot grpmax-eligible	2.37%	42
Remaining individualsnot grpmax-eligible	1.9%	53
European (non-Finnish)	1.29%	78
Middle Eastern	0.957%	105
Admixed American	0.387%	259
African / African-American	0.261%	383
Amishnot grpmax-eligible	0.219%	456

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: BAZ2B
Protein: p.Ala840=
Coding: c.2520A>C
MANE Select: NM_013450
dbSNP: rs3755433
Type: single nucleotide variant
Location: chr2:159412492 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 840: an α-helix

Full BAZ2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BAZ2B-related disorder

Similar variants

BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same condition
BAZ2B c.5797-1G>C Likely pathogenic ★ same condition
BAZ2B p.Glu1854Ter Likely pathogenic ★ same condition
BAZ2B p.Leu718Phe Likely pathogenic ★ ⚠ same condition
BAZ2B c.2255+10A>G Uncertain significance ★ same condition
BAZ2B c.2466+2T>G Uncertain significance ★ same condition
BAZ2B p.Arg855Ter 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/baz2b-p-ala840 (accessed [today's date]).

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