16-50334752-G-A

Variant names:

• chr16-50334752-G-A
• rs1062348
• NM_013263.5:c.846C>T

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 13 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013263.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD7	NM_013263.5	MANE Select	c.846C>T	p.Ala282Ala	synonymous	Exon 7 of 17	NP_037395.2
	BRD7	NM_001438173.1		c.897C>T	p.Ala299Ala	synonymous	Exon 7 of 17	NP_001425102.1
	BRD7	NM_001437990.1		c.897C>T	p.Ala299Ala	synonymous	Exon 7 of 17	NP_001424919.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD7	ENST00000394688.8	TSL:1 MANE Select	c.846C>T	p.Ala282Ala	synonymous	Exon 7 of 17	ENSP00000378180.3
	BRD7	ENST00000394689.2	TSL:1	c.846C>T	p.Ala282Ala	synonymous	Exon 7 of 17	ENSP00000378181.2
	BRD7	ENST00000710357.1		c.969C>T	p.Ala323Ala	synonymous	Exon 7 of 17	ENSP00000518228.1

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

GnomAD2 exomes AF: 0.156 AC: 39148 AN: 250694 AF XY: 0.152

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

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

GnomAD4 genome AF: 0.174 AC: 26348 AN: 151860 Hom.: 2998 Cov.: 32 AF XY: 0.179 AC XY: 13261 AN XY: 74206

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: 17 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7175 AN: 67972

Other (OTH) AF: 0.144 AC: 304 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.32
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)

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

Other links and lift over

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