chr6-32976202-C-CT

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]

Genome browser will be placed here

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
BRD2NM_005104.4 linkc.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
BRD2ENST00000374825.9 linkc.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.:
0
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.:
45
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
0
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
0
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.:
0
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
0
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
0
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)

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

Other links and lift over

dbSNP: rs2066741; hg19: chr6-32943979; COSMIC: COSV104425873; COSMIC: COSV104425873; API