chr16-50329153-A-G

Variant names:

• chr16-50329153-A-G
• rs34582796
• NM_013263.5:c.1012-409T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013263.5(BRD7):​c.1012-409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,984 control chromosomes in the GnomAD database, including 4,752 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 0.24 (4752 hom., cov: 32)
• Consequence: BRD7 NM_013263.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 2 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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.1012-409T>C		intron	N/A	NP_037395.2
	BRD7	NM_001438173.1		c.1063-409T>C		intron	N/A	NP_001425102.1
	BRD7	NM_001437990.1		c.1063-409T>C		intron	N/A	NP_001424919.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD7	ENST00000394688.8	TSL:1 MANE Select	c.1012-409T>C		intron	N/A	ENSP00000378180.3
	BRD7	ENST00000394689.2	TSL:1	c.1012-409T>C		intron	N/A	ENSP00000378181.2
	BRD7	ENST00000710357.1		c.1135-409T>C		intron	N/A	ENSP00000518228.1

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36701 AN: 151866 Hom.: 4745 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.242 AC: 36733 AN: 151984 Hom.: 4752 Cov.: 32 AF XY: 0.243 AC XY: 18084 AN XY: 74290

African (AFR) AF: 0.312 AC: 12915 AN: 41416

American (AMR) AF: 0.308 AC: 4706 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1568 AN: 5152

South Asian (SAS) AF: 0.300 AC: 1444 AN: 4814

European-Finnish (FIN) AF: 0.157 AC: 1663 AN: 10590

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.190 AC: 12933 AN: 67966

Other (OTH) AF: 0.230 AC: 485 AN: 2106

Alfa AF: 0.228 Hom.: 1197

Bravo AF: 0.253

Asia WGS AF: 0.293 AC: 1017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.54
PhyloP100		-0.30
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: rs34582796; hg19: chr16-50363064;