rs1062348

chr16-50334752-G-Achr16-50334752-G-Cchr16-50334752-G-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_013263.5(BRD7):c.846C>T(p.Ala282=) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

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]

ACMG classification

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/exons	MANE	UniProt
BRD7	NM_013263.5	c.846C>T	p.Ala282=	synonymous_variant	7/17	ENST00000394688.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRD7	ENST00000394688.8	c.846C>T	p.Ala282=	synonymous_variant	7/17	1	NM_013263.5	P4

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26329 AN: 151742 Hom.: 2999 Cov.: 32

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

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.: 32 AF XY: 0.129 AC XY: 93497 AN XY: 726842

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.: 32 AF XY: 0.179 AC XY: 13261 AN XY: 74206

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

Other links and lift over

dbSNP: rs1062348; hg19: chr16-50368663; COSMIC: COSV67159766;