3-9741676-C-T

Position:

• chr3-9741676-C-T

Variant summary

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

The NM_001003694.2(BRPF1):​c.1854+237C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 149,502 control chromosomes in the GnomAD database, including 5,811 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 0.27 (5811 hom., cov: 30)
• Consequence: BRPF1 NM_001003694.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

BRPF1 (HGNC:14255): (bromodomain and PHD finger containing 1) This gene encodes a bromodomain, PHD finger and chromo/Tudor-related Pro-Trp-Trp-Pro (PWWP) domain containing protein. The encoded protein is a component of the MOZ/MORF histone acetyltransferase complexes which function as a transcriptional regulators. This protein binds to the catalytic MYST domains of the MOZ and MORF proteins and may play a role in stimulating acetyltransferase and transcriptional activity of the complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRPF1	NM_001003694.2	c.1854+237C>T		intron_variant		ENST00000383829.7	NP_001003694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRPF1	ENST00000383829.7	c.1854+237C>T		intron_variant		1	NM_001003694.2	ENSP00000373340	A1

Frequencies

GnomAD3 genomes AF: 0.272 AC: 40678 AN: 149448 Hom.: 5791 Cov.: 30

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0888

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.273 AC: 40740 AN: 149502 Hom.: 5811 Cov.: 30 AF XY: 0.272 AC XY: 19738 AN XY: 72620

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0890

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.274

Alfa AF: 0.287 Hom.: 3046

Bravo AF: 0.261

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.85
DANN	Benign	0.61

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: rs159154; hg19: chr3-9783360;