chr16-50337827-T-C

Variant names:

• chr16-50337827-T-C
• rs11644386
• NM_013263.5:c.702+2149A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_013263.5(BRD7):​c.702+2149A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,554 control chromosomes in the GnomAD database, including 5,915 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 0.26 (5915 hom., cov: 30)
• Consequence: BRD7 NM_013263.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 17 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD7	NM_013263.5	MANE Select	c.702+2149A>G		intron	N/A	NP_037395.2
	BRD7	NM_001438173.1		c.753+2149A>G		intron	N/A	NP_001425102.1
	BRD7	NM_001437990.1		c.753+2149A>G		intron	N/A	NP_001424919.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD7	ENST00000394688.8	TSL:1 MANE Select	c.702+2149A>G		intron	N/A	ENSP00000378180.3
	BRD7	ENST00000394689.2	TSL:1	c.702+2149A>G		intron	N/A	ENSP00000378181.2
	BRD7	ENST00000710357.1		c.825+2149A>G		intron	N/A	ENSP00000518228.1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38725 AN: 151436 Hom.: 5906 Cov.: 30

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.235

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.256 AC: 38783 AN: 151554 Hom.: 5915 Cov.: 30 AF XY: 0.257 AC XY: 18997 AN XY: 74010

African (AFR) AF: 0.416 AC: 17170 AN: 41230

American (AMR) AF: 0.304 AC: 4627 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 719 AN: 3464

East Asian (EAS) AF: 0.307 AC: 1581 AN: 5156

South Asian (SAS) AF: 0.285 AC: 1369 AN: 4802

European-Finnish (FIN) AF: 0.134 AC: 1401 AN: 10478

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11163 AN: 67896

Other (OTH) AF: 0.237 AC: 498 AN: 2098

Alfa AF: 0.210 Hom.: 5861

Bravo AF: 0.272

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs11644386; hg19: chr16-50371738;