Variant rs11908 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005104.4(BRD2):c.1200+33G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 1,573,522 control chromosomes in the GnomAD database, including 98,723 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 8408 hom., cov: 32)

Exomes 𝑓: 0.35 ( 90315 hom. )

Consequence

BRD2
NM_005104.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.27

Variant links:

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]

BRD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRD2	NM_005104.4 linkuse as main transcript	c.1200+33G>A		intron_variant		ENST00000374825.9	NP_005095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRD2	ENST00000374825.9 linkuse as main transcript	c.1200+33G>A		intron_variant		1	NM_005104.4	ENSP00000363958	P2	P25440-1

Frequencies

GnomAD3 genomes

AF:

0.318

AC:

48371

AN:

151994

Hom.:

8408

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.374

Gnomad AMR

AF:

0.282

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.313

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.279

GnomAD3 exomes

AF:

0.344

AC:

73767

AN:

214648

Hom.:

13420

AF XY:

0.347

AC XY:

40739

AN XY:

117338

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.291

Gnomad ASJ exome

AF:

0.347

Gnomad EAS exome

AF:

0.175

Gnomad SAS exome

AF:

0.333

Gnomad FIN exome

AF:

0.516

Gnomad NFE exome

AF:

0.380

Gnomad OTH exome

AF:

0.340

GnomAD4 exome

AF:

0.351

AC:

498656

AN:

1421410

Hom.:

90315

Cov.:

AF XY:

0.352

AC XY:

247268

AN XY:

703018

show subpopulations

Gnomad4 AFR exome

AF:

0.192

Gnomad4 AMR exome

AF:

0.282

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.213

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.360

Gnomad4 OTH exome

AF:

0.325

GnomAD4 genome

AF:

0.318

AC:

48381

AN:

152112

Hom.:

8408

Cov.:

AF XY:

0.323

AC XY:

24024

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.201

Gnomad4 AMR

AF:

0.282

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.313

Gnomad4 FIN

AF:

0.516

Gnomad4 NFE

AF:

0.376

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.356

Hom.:

17240

Bravo

AF:

0.291

Asia WGS

AF:

0.240

AC:

837

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over