Genetic Variant BRD7:p.Ala282Ala (chr16-50334752-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_013263.5(BRD7):c.846C>T(p.Ala282Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,612,936 control chromosomes in the GnomAD database, including 17,977 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 0.17 ( 2998 hom., cov: 32)

Exomes 𝑓: 0.13 ( 14979 hom. )

Consequence

BRD7
NM_013263.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.176

Variant links:

Genes affected

BRD7 (HGNC:14310): (bromodomain containing 7) This gene encodes a protein which is a member of the bromodomain-containing protein family. The product of this gene has been identified as a component of one form of the SWI/SNF chromatin remodeling complex, and as a protein which interacts with p53 and is required for p53-dependent oncogene-induced senescence which prevents tumor growth. Pseudogenes have been described on chromosomes 2, 3, 6, 13 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

BRD7 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP7

Synonymous conserved (PhyloP=-0.176 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRD7	NM_013263.5 link	c.846C>T	p.Ala282Ala	synonymous_variant	Exon 7 of 17	ENST00000394688.8	NP_037395.2	Q9NPI1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRD7	ENST00000394688.8 link	c.846C>T	p.Ala282Ala	synonymous_variant	Exon 7 of 17	1	NM_013263.5	ENSP00000378180.3		Q9NPI1-1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26329

AN:

151742

Hom.:

2999

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.101

Gnomad ASJ

AF:

0.0367

Gnomad EAS

AF:

0.487

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.144

GnomAD2 exomes

AF:

0.156

AC:

39148

AN:

250694

AF XY:

0.152

show subpopulations

Gnomad AFR exome

AF:

0.273

Gnomad AMR exome

AF:

0.0936

Gnomad ASJ exome

AF:

0.0351

Gnomad EAS exome

AF:

0.486

Gnomad FIN exome

AF:

0.214

Gnomad NFE exome

AF:

0.102

Gnomad OTH exome

AF:

0.125

GnomAD4 exome

AF:

0.129

AC:

188165

AN:

1461076

Hom.:

14979

Cov.:

AF XY:

0.129

AC XY:

93497

AN XY:

726842

show subpopulations

African (AFR)

AF:

0.281

AC:

9384

AN:

33354

American (AMR)

AF:

0.0937

AC:

4188

AN:

44706

Ashkenazi Jewish (ASJ)

AF:

0.0352

AC:

919

AN:

26128

East Asian (EAS)

AF:

0.447

AC:

17719

AN:

39656

South Asian (SAS)

AF:

0.172

AC:

14794

AN:

86220

European-Finnish (FIN)

AF:

0.210

AC:

11210

AN:

53362

Middle Eastern (MID)

AF:

0.0698

AC:

402

AN:

5760

European-Non Finnish (NFE)

AF:

0.109

AC:

120863

AN:

1111548

Other (OTH)

AF:

0.144

AC:

8686

AN:

60342

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

8264

16528

24791

33055

41319

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.174

AC:

26348

AN:

151860

Hom.:

2998

Cov.:

AF XY:

0.179

AC XY:

13261

AN XY:

74206

show subpopulations

African (AFR)

AF:

0.277

AC:

11472

AN:

41360

American (AMR)

AF:

0.101

AC:

1536

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.0367

AC:

127

AN:

3464

East Asian (EAS)

AF:

0.487

AC:

2508

AN:

5154

South Asian (SAS)

AF:

0.194

AC:

932

AN:

4814

European-Finnish (FIN)

AF:

0.214

AC:

2254

AN:

10536

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7175

AN:

67972

Other (OTH)

AF:

0.144

AC:

304

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1031

2063

3094

4126

5157

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.110

Hom.:

452

Bravo

AF:

0.171

Asia WGS

AF:

0.322

AC:

1119

AN:

3478

EpiCase

AF:

0.0955

EpiControl

AF:

0.0929

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.32

(source)

DANN

Benign

0.78

PhyloP100

-0.18

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

LitVar

Below is the list of publications found by LitVar for variant 16:50334752 G>A . It may be empty.

chr16-50334752-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over