rs8104223

Positions:

• chr19-15252666-A-G
• chr19-15252666-A-T

Variant summary

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

The NM_001379291.1(BRD4):​c.2158+1486T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,216 control chromosomes in the GnomAD database, including 4,396 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 0.21 (4396 hom., cov: 32)
• Consequence: BRD4 NM_001379291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

Genes affected

BRD4 (HGNC:13575): (bromodomain containing 4) The protein encoded by this gene is homologous to the murine protein MCAP, which associates with chromosomes during mitosis, and to the human RING3 protein, a serine/threonine kinase. Each of these proteins contains two bromodomains, a conserved sequence motif which may be involved in chromatin targeting. This gene has been implicated as the chromosome 19 target of translocation t(15;19)(q13;p13.1), which defines an upper respiratory tract carcinoma in young people. Two alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRD4	NM_001379291.1	c.2158+1486T>C		intron_variant		ENST00000679869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRD4	ENST00000679869.1	c.2158+1486T>C		intron_variant			NM_001379291.1	P1
BRD4	ENST00000263377.6	c.2158+1486T>C		intron_variant		1		P1
BRD4	ENST00000371835.8	c.2158+1486T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32602 AN: 152098 Hom.: 4396 Cov.: 32

Gnomad AFR AF: 0.0788

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.214 AC: 32600 AN: 152216 Hom.: 4396 Cov.: 32 AF XY: 0.208 AC XY: 15459 AN XY: 74430

Gnomad4 AFR AF: 0.0786

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.255

Alfa AF: 0.272 Hom.: 2136

Bravo AF: 0.207

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.76

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: rs8104223; hg19: chr19-15363477;