rs740

Positions:

• chr2-159434566-C-T

Variant summary

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

The NM_013450.4(BAZ2B):​c.1294-1203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,874 control chromosomes in the GnomAD database, including 9,800 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 0.32 (9799 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

BAZ2B (HGNC:963): (bromodomain adjacent to zinc finger domain 2B) This gene belongs to the bromodomain gene family. Members of this gene family encode proteins that are integral components of chromatin remodeling complexes. The encoded protein showed strong preference for the activating H3K14Ac mark in a histone peptide screen, suggesting a potential role in transcriptional activation. This gene may be associated with susceptibility to sudden cardiac death (SCD). [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAZ2B	NM_013450.4	c.1294-1203G>A		intron_variant		ENST00000392783.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ2B	ENST00000392783.7	c.1294-1203G>A		intron_variant		5	NM_013450.4	P1
BAZ2B	ENST00000392782.5	c.1288-1203G>A		intron_variant		1
BAZ2B	ENST00000472953.1	n.988G>A		non_coding_transcript_exon_variant	1/8	5

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49210 AN: 151748 Hom.: 9795 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.500 AC: 4 AN: 8 Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.324 AC: 49232 AN: 151866 Hom.: 9799 Cov.: 32 AF XY: 0.314 AC XY: 23290 AN XY: 74232

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.345

Alfa AF: 0.385 Hom.: 1600

Bravo AF: 0.316

Asia WGS AF: 0.240 AC: 838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.4
DANN	Benign	0.70

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: rs740; hg19: chr2-160291077;