rs2066741

chr6-32976202-C-CT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_005104.4(BRD2):c.610+34dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,610,696 control chromosomes in the GnomAD database, including 195,390 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.50 (19347 hom., cov: 0)
  • Exomes 𝑓: 0.49 (176043 hom.)
• Consequence: BRD2 NM_005104.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602

Genes affected

BRD2 (HGNC:1103): (bromodomain containing 2) This gene encodes a transcriptional regulator that belongs to the BET (bromodomains and extra terminal domain) family of proteins. This protein associates with transcription complexes and with acetylated chromatin during mitosis, and it selectively binds to the acetylated lysine-12 residue of histone H4 via its two bromodomains. The gene maps to the major histocompatability complex (MHC) class II region on chromosome 6p21.3, but sequence comparison suggests that the protein is not involved in the immune response. This gene has been implicated in juvenile myoclonic epilepsy, a common form of epilepsy that becomes apparent in adolescence. Multiple alternatively spliced variants have been described for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRD2	NM_005104.4	c.610+34dup		intron_variant		ENST00000374825.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRD2	ENST00000374825.9	c.610+34dup		intron_variant		1	NM_005104.4	P2

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75910 AN: 151826 Hom.: 19335 Cov.: 0

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.487

GnomAD3 exomes AF: 0.470 AC: 115279 AN: 245122 Hom.: 27820 AF XY: 0.468 AC XY: 62441 AN XY: 133510

Gnomad AFR exome AF: 0.531

Gnomad AMR exome AF: 0.373

Gnomad ASJ exome AF: 0.515

Gnomad EAS exome AF: 0.349

Gnomad SAS exome AF: 0.398

Gnomad FIN exome AF: 0.611

Gnomad NFE exome AF: 0.500

Gnomad OTH exome AF: 0.475

GnomAD4 exome AF: 0.488 AC: 711894 AN: 1458752 Hom.: 176043 Cov.: 45 AF XY: 0.486 AC XY: 352706 AN XY: 725474

Gnomad4 AFR exome AF: 0.544

Gnomad4 AMR exome AF: 0.374

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.411

Gnomad4 SAS exome AF: 0.393

Gnomad4 FIN exome AF: 0.609

Gnomad4 NFE exome AF: 0.496

Gnomad4 OTH exome AF: 0.473

GnomAD4 genome AF: 0.500 AC: 75946 AN: 151944 Hom.: 19347 Cov.: 0 AF XY: 0.500 AC XY: 37093 AN XY: 74246

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.484

Alfa AF: 0.513 Hom.: 3700

Bravo AF: 0.485

Asia WGS AF: 0.375 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2066741; hg19: chr6-32943979;