rs4665058

Positions:

• chr2-159333698-A-C
• chr2-159333698-A-G
• chr2-159333698-A-T

Variant summary

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

The NM_013450.4(BAZ2B):​c.5797-1012T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,102 control chromosomes in the GnomAD database, including 63,584 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 0.91 (63584 hom., cov: 32)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.5797-1012T>G		intron_variant		ENST00000392783.7	NP_038478.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ2B	ENST00000392783.7	c.5797-1012T>G		intron_variant		5	NM_013450.4	ENSP00000376534	P1
BAZ2B	ENST00000392782.5	c.5689-1012T>G		intron_variant		1		ENSP00000376533
BAZ2B	ENST00000474437.1	n.337-1012T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137862 AN: 151984 Hom.: 63527 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.907 AC: 137975 AN: 152102 Hom.: 63584 Cov.: 32 AF XY: 0.909 AC XY: 67612 AN XY: 74374

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.967

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.938

Alfa AF: 0.976 Hom.: 78886

Bravo AF: 0.898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.67
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs4665058; hg19: chr2-160190209;