2-159393260-T-C

Position:

• chr2-159393260-T-C

Variant summary

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

The NM_013450.4(BAZ2B):​c.3075+2509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,012 control chromosomes in the GnomAD database, including 37,008 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 0.66 (37008 hom., cov: 31)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.3075+2509A>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.3075+2509A>G		intron_variant		5	NM_013450.4	ENSP00000376534	P1
	ENST00000420020.5	n.220+1046T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100935 AN: 151894 Hom.: 37005 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.664 AC: 100954 AN: 152012 Hom.: 37008 Cov.: 31 AF XY: 0.664 AC XY: 49351 AN XY: 74290

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.847

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.674

Alfa AF: 0.791 Hom.: 27897

Bravo AF: 0.629

Asia WGS AF: 0.663 AC: 2304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.46

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: rs12692550; hg19: chr2-160249771;