9-134060541-G-T

Variant names:

• chr9-134060541-G-T
• rs11789898
• NM_007371.4:c.-113-6951C>A

Variant summary

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

The NM_007371.4(BRD3):​c.-113-6951C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,828 control chromosomes in the GnomAD database, including 1,796 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 0.14 (1796 hom., cov: 31)
• Consequence: BRD3 NM_007371.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

Genes affected

BRD3 (HGNC:1104): (bromodomain containing 3) This gene was identified based on its homology to the gene encoding the RING3 protein, a serine/threonine kinase. The gene localizes to 9q34, a region which contains several major histocompatibility complex (MHC) genes. The function of the encoded protein is not known. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BRD3	NM_007371.4	c.-113-6951C>A		intron_variant	Intron 1 of 11	ENST00000303407.12	NP_031397.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BRD3	ENST00000303407.12	c.-113-6951C>A		intron_variant	Intron 1 of 11	1	NM_007371.4	ENSP00000305918.6
BRD3	ENST00000371834.6	c.-113-6951C>A		intron_variant	Intron 1 of 9	1		ENSP00000360900.2

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21295 AN: 151710 Hom.: 1796 Cov.: 31

Gnomad AFR AF: 0.0539

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0988

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.140 AC: 21293 AN: 151828 Hom.: 1796 Cov.: 31 AF XY: 0.143 AC XY: 10591 AN XY: 74166

Gnomad4 AFR AF: 0.0538

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.0982

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.149

Alfa AF: 0.0851 Hom.: 116

Bravo AF: 0.133

Asia WGS AF: 0.121 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.57

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: rs11789898; hg19: chr9-136925663;