rs11644043

chr16-50327466-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_013263.5(BRD7):c.1088-1075A>G 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 152,136 control chromosomes in the GnomAD database, including 4,767 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 (4767 hom., cov: 32)
• Consequence: BRD7 NM_013263.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.421

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRD7	NM_013263.5	c.1088-1075A>G		intron_variant		ENST00000394688.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRD7	ENST00000394688.8	c.1088-1075A>G		intron_variant		1	NM_013263.5	P4
BRD7	ENST00000394689.2	c.1088-1075A>G		intron_variant		1		A1
BRD7	ENST00000710356.1	c.1139-1075A>G		intron_variant
BRD7	ENST00000710357.1	c.1211-1075A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36764 AN: 152018 Hom.: 4760 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.242 AC: 36797 AN: 152136 Hom.: 4767 Cov.: 32 AF XY: 0.244 AC XY: 18123 AN XY: 74394

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.232

Alfa AF: 0.203 Hom.: 5544

Bravo AF: 0.253

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.6
Dann	Benign	0.79

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: rs11644043; hg19: chr16-50361377;