Is BRD2 p.Lys31= (c.93G>A) pathogenic?

BRD2 p.Lys31= (c.93G>A) is classified Benign in BRD2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-17). Common (popmax 78.1%, afr) — too common for a highly-penetrant pathogenic allele; Associated with BRD2-related disorder.

What condition is associated with BRD2 p.Lys31= (c.93G>A)?

BRD2 p.Lys31= (c.93G>A) is associated with BRD2-related disorder (ClinVar).

BRD2 p.Lys31=

Q: How common is BRD2 p.Lys31= (c.93G>A) in the general population?

BRD2 p.Lys31= (c.93G>A) is common (popmax 78.1%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.93G>A · rs516535 · VCV3058972

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 78.1%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

BRD2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.089	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP -0.44, phastCons 1
Overall
CADD	6.704	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 78.1% African / African-American · 58,593/74,986 alleles

Filtering AF 77.6% ClinGen BA1/BS1 input FAF95, joint · FAF99 77.4%

Overall 59.3% 956,363/1,613,806 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	78.1%	1
Finnishnot grpmax-eligible	63.1%	2
Ashkenazi Jewishnot grpmax-eligible	60.4%	2
European (non-Finnish)	59%	2
Middle Eastern	59%	2
Remaining individualsnot grpmax-eligible	58.5%	2
South Asian	52.8%	2
East Asian	52.5%	2
Admixed American	51.9%	2
Amishnot grpmax-eligible	51.8%	2

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: BRD2
Protein: p.Lys31=
Coding: c.93G>A
MANE Select: NM_005104
dbSNP: rs516535
Type: single nucleotide variant
Location: chr6:32974525 (GRCh38)
Gene constraint: LOEUF 0.28 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 65.70 · 169 PDB

Full BRD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BRD2-related disorder

Similar variants

BRD2 c.334-10T>C Benign same condition
BRD2 c.472-5C>T Likely benign same condition
BRD2 p.Ala474Val Benign same condition
BRD2 p.Asp570= Benign same condition
BRD2 p.Lys751= Likely benign same condition
BRD2 p.Ser603= Benign same condition
BRD2 p.Tyr153= Likely benign same condition
BRD2 p.Pro12Leu 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/brd2-p-lys31 (accessed [today's date]).

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