Genetic Variant NM_005104.4:c.610+34dupT (chr6-32976202-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005104.4(BRD2):c.610+34dupT 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

6 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BRD2	NM_005104.4 link	c.610+34dupT		intron_variant	Intron 5 of 12	ENST00000374825.9	NP_005095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRD2	ENST00000374825.9 link	c.610+34dupT		intron_variant	Intron 5 of 12	1	NM_005104.4	ENSP00000363958.4		P25440-1

Frequencies

GnomAD3 genomes

AF:

0.500

AC:

75910

AN:

151826

Hom.:

19335

Cov.:

show subpopulations

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

GnomAD2 exomes

AF:

0.470

AC:

115279

AN:

245122

AF XY:

0.468

show subpopulations

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 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.:

AF XY:

0.486

AC XY:

352706

AN XY:

725474

show subpopulations

African (AFR)

AF:

0.544

AC:

18153

AN:

33362

American (AMR)

AF:

0.374

AC:

16630

AN:

44504

Ashkenazi Jewish (ASJ)

AF:

0.508

AC:

13224

AN:

26038

East Asian (EAS)

AF:

0.411

AC:

16290

AN:

39660

South Asian (SAS)

AF:

0.393

AC:

33801

AN:

86090

European-Finnish (FIN)

AF:

0.609

AC:

31848

AN:

52292

Middle Eastern (MID)

AF:

0.476

AC:

2741

AN:

5762

European-Non Finnish (NFE)

AF:

0.496

AC:

550701

AN:

1110760

Other (OTH)

AF:

0.473

AC:

28506

AN:

60284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

21807

43614

65422

87229

109036

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15952

31904

47856

63808

79760

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.500

AC:

75946

AN:

151944

Hom.:

19347

Cov.:

AF XY:

0.500

AC XY:

37093

AN XY:

74246

show subpopulations

African (AFR)

AF:

0.527

AC:

21820

AN:

41406

American (AMR)

AF:

0.418

AC:

6386

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.519

AC:

1802

AN:

3470

East Asian (EAS)

AF:

0.357

AC:

1845

AN:

5172

South Asian (SAS)

AF:

0.393

AC:

1894

AN:

4818

European-Finnish (FIN)

AF:

0.611

AC:

6446

AN:

10542

Middle Eastern (MID)

AF:

0.534

AC:

157

AN:

294

European-Non Finnish (NFE)

AF:

0.503

AC:

34145

AN:

67936

Other (OTH)

AF:

0.484

AC:

1020

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1914

3829

5743

7658

9572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.60

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over