Variant 6-32974446-G-GT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_005104.4(BRD2):c.30-14dup variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 1,600,636 control chromosomes in the GnomAD database, including 853 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.024 ( 62 hom., cov: 32)

Exomes 𝑓: 0.031 ( 791 hom. )

Consequence

BRD2
NM_005104.4 splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:2

Conservation

PhyloP100: 0.609

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 -9 ACMG points.

BP6

Variant 6-32974446-G-GT is Benign according to our data. Variant chr6-32974446-G-GT is described in ClinVar as [Benign]. Clinvar id is 1175005.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0236 (3599/152286) while in subpopulation SAS AF= 0.039 (188/4824). AF 95% confidence interval is 0.0344. There are 62 homozygotes in gnomad4. There are 1719 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 62 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRD2	NM_005104.4 linkuse as main transcript	c.30-14dup		splice_polypyrimidine_tract_variant, 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.30-14dup		splice_polypyrimidine_tract_variant, intron_variant		1	NM_005104.4	ENSP00000363958	P2	P25440-1

Frequencies

GnomAD3 genomes

AF:

0.0237

AC:

3599

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00649

Gnomad AMI

AF:

0.0110

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0115

Gnomad EAS

AF:

0.0241

Gnomad SAS

AF:

0.0385

Gnomad FIN

AF:

0.0141

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0351

Gnomad OTH

AF:

0.0268

GnomAD3 exomes

AF:

0.0291

AC:

7115

AN:

244708

Hom.:

126

AF XY:

0.0302

AC XY:

4009

AN XY:

132572

show subpopulations

Gnomad AFR exome

AF:

0.00630

Gnomad AMR exome

AF:

0.0251

Gnomad ASJ exome

AF:

0.0131

Gnomad EAS exome

AF:

0.0240

Gnomad SAS exome

AF:

0.0437

Gnomad FIN exome

AF:

0.0135

Gnomad NFE exome

AF:

0.0346

Gnomad OTH exome

AF:

0.0350

GnomAD4 exome

AF:

0.0314

AC:

45496

AN:

1448350

Hom.:

791

Cov.:

AF XY:

0.0320

AC XY:

22985

AN XY:

718630

show subpopulations

Gnomad4 AFR exome

AF:

0.00484

Gnomad4 AMR exome

AF:

0.0255

Gnomad4 ASJ exome

AF:

0.0131

Gnomad4 EAS exome

AF:

0.0162

Gnomad4 SAS exome

AF:

0.0446

Gnomad4 FIN exome

AF:

0.0151

Gnomad4 NFE exome

AF:

0.0334

Gnomad4 OTH exome

AF:

0.0283

GnomAD4 genome

AF:

0.0236

AC:

3599

AN:

152286

Hom.:

Cov.:

AF XY:

0.0231

AC XY:

1719

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00647

Gnomad4 AMR

AF:

0.0243

Gnomad4 ASJ

AF:

0.0115

Gnomad4 EAS

AF:

0.0239

Gnomad4 SAS

AF:

0.0390

Gnomad4 FIN

AF:

0.0141

Gnomad4 NFE

AF:

0.0351

Gnomad4 OTH

AF:

0.0265

Alfa

AF:

0.0291

Hom.:

Bravo

AF:

0.0233

Asia WGS

AF:

0.0480

AC:

169

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over