NM_013263.5:c.702+2149A>G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRD7	NM_013263.5	c.702+2149A>G		intron_variant	Intron 6 of 16	ENST00000394688.8	NP_037395.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRD7	ENST00000394688.8	c.702+2149A>G		intron_variant	Intron 6 of 16	1	NM_013263.5	ENSP00000378180.3

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

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.134

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.237

Alfa AF: 0.180 Hom.: 2797

Bravo AF: 0.272

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	-0.45
CADD	Benign	12
DANN	Benign	0.68

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

Publications

LitVar

Other links and lift over

dbSNP: rs11644386; hg19: chr16-50371738;