Variant 6-32978356-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_005104.4(BRD2):c.1809T>C(p.Ser603Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 1,612,632 control chromosomes in the GnomAD database, including 102,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.32 ( 8470 hom., cov: 32)

Exomes 𝑓: 0.35 ( 94051 hom. )

Consequence

BRD2
NM_005104.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.426

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:

BRD2 (HGNC:):

BRD2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 6-32978356-T-C is Benign according to our data. Variant chr6-32978356-T-C is described in ClinVar as [Benign]. Clinvar id is 3059565.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.426 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 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.1809T>C	p.Ser603Ser	synonymous_variant	10/13	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.1809T>C	p.Ser603Ser	synonymous_variant	10/13	1	NM_005104.4	ENSP00000363958.4		P25440-1

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48531

AN:

151942

Hom.:

8470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.373

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.333

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.370

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.279

GnomAD3 exomes

AF:

0.342

AC:

83919

AN:

245206

Hom.:

15363

AF XY:

0.345

AC XY:

46206

AN XY:

133844

show subpopulations

Gnomad AFR exome

AF:

0.196

Gnomad AMR exome

AF:

0.287

Gnomad ASJ exome

AF:

0.336

Gnomad EAS exome

AF:

0.174

Gnomad SAS exome

AF:

0.324

Gnomad FIN exome

AF:

0.516

Gnomad NFE exome

AF:

0.379

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.353

AC:

515638

AN:

1460572

Hom.:

94051

Cov.:

AF XY:

0.354

AC XY:

257267

AN XY:

726596

show subpopulations

Gnomad4 AFR exome

AF:

0.193

Gnomad4 AMR exome

AF:

0.280

Gnomad4 ASJ exome

AF:

0.338

Gnomad4 EAS exome

AF:

0.213

Gnomad4 SAS exome

AF:

0.318

Gnomad4 FIN exome

AF:

0.513

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.326

GnomAD4 genome

AF:

0.319

AC:

48541

AN:

152060

Hom.:

8470

Cov.:

AF XY:

0.324

AC XY:

24084

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.202

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.333

Gnomad4 EAS

AF:

0.190

Gnomad4 SAS

AF:

0.314

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.379

Gnomad4 OTH

AF:

0.277

Alfa

AF:

0.356

Hom.:

18347

Bravo

AF:

0.293

Asia WGS

AF:

0.240

AC:

839

AN:

3478

EpiCase

AF:

0.369

EpiControl

AF:

0.357

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BRD2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

4.4

DANN

Benign

0.67

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.6

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