dbSNP rs1062348: BRD7:p.Ala282Ala (chr16-50334752-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -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 made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.156

AC:

39148

AN:

250694

Hom.:

4419

AF XY:

0.152

AC XY:

20561

AN XY:

135540

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 SAS exome

AF:

0.172

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

Gnomad4 AFR exome

AF:

0.281

Gnomad4 AMR exome

AF:

0.0937

Gnomad4 ASJ exome

AF:

0.0352

Gnomad4 EAS exome

AF:

0.447

Gnomad4 SAS exome

AF:

0.172

Gnomad4 FIN exome

AF:

0.210

Gnomad4 NFE exome

AF:

0.109

Gnomad4 OTH exome

AF:

0.144

GnomAD4 genome

AF:

0.174

AC:

26348

AN:

151860

Hom.:

2998

Cov.:

AF XY:

0.179

AC XY:

13261

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.0367

Gnomad4 EAS

AF:

0.487

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.106

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.111

Hom.:

413

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

DANN

Benign

0.78

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over