NM_005104.4:c.30-329G>T

Variant names:

• chr6-32974133-G-T
• rs620202
• NM_005104.4:c.30-329G>T

Variant summary

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

The NM_005104.4(BRD2):​c.30-329G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,068 control chromosomes in the GnomAD database, including 4,940 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 (4940 hom., cov: 32)
• Consequence: BRD2 NM_005104.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 29 publications found

Genes affected

BRD2 (HGNC:1103): (bromodomain containing 2) This gene encodes a transcriptional regulator that belongs to the BET (bromodomains and extra terminal domain) family of proteins. This protein associates with transcription complexes and with acetylated chromatin during mitosis, and it selectively binds to the acetylated lysine-12 residue of histone H4 via its two bromodomains. The gene maps to the major histocompatability complex (MHC) class II region on chromosome 6p21.3, but sequence comparison suggests that the protein is not involved in the immune response. This gene has been implicated in juvenile myoclonic epilepsy, a common form of epilepsy that becomes apparent in adolescence. Multiple alternatively spliced variants have been described for this gene. [provided by RefSeq, Dec 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005104.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD2	NM_005104.4	MANE Select	c.30-329G>T		intron	N/A	NP_005095.1	P25440-1
	BRD2	NM_001199455.1		c.30-329G>T		intron	N/A	NP_001186384.1	P25440-2
	BRD2	NM_001113182.3		c.30-329G>T		intron	N/A	NP_001106653.1	P25440-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRD2	ENST00000374825.9	TSL:1 MANE Select	c.30-329G>T		intron	N/A	ENSP00000363958.4	P25440-1
	BRD2	ENST00000395287.5	TSL:1	c.30-329G>T		intron	N/A	ENSP00000378702.1	P25440-2
	BRD2	ENST00000449025.5	TSL:1	c.45-329G>T		intron	N/A	ENSP00000409613.1	H0Y6K2

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35794 AN: 151950 Hom.: 4939 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.235 AC: 35802 AN: 152068 Hom.: 4940 Cov.: 32 AF XY: 0.243 AC XY: 18069 AN XY: 74296

African (AFR) AF: 0.110 AC: 4579 AN: 41498

American (AMR) AF: 0.210 AC: 3211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1033 AN: 3470

East Asian (EAS) AF: 0.178 AC: 921 AN: 5178

South Asian (SAS) AF: 0.260 AC: 1249 AN: 4812

European-Finnish (FIN) AF: 0.457 AC: 4833 AN: 10568

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19148 AN: 67948

Other (OTH) AF: 0.201 AC: 422 AN: 2104

Alfa AF: 0.263 Hom.: 14741

Bravo AF: 0.208

Asia WGS AF: 0.203 AC: 708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		1.4
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: rs620202; hg19: chr6-32941910;