rs10489997

Positions:

• chr2-159548987-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.-3+6836G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,016 control chromosomes in the GnomAD database, including 9,668 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 (9668 hom., cov: 32)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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]

BAZ2B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.-3+6836G>A		intron_variant		ENST00000392783.7	NP_038478.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ2B	ENST00000392783.7	c.-3+6836G>A		intron_variant		5	NM_013450.4	ENSP00000376534.2

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48395 AN: 151898 Hom.: 9666 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.318 AC: 48413 AN: 152016 Hom.: 9668 Cov.: 32 AF XY: 0.318 AC XY: 23612 AN XY: 74304

Gnomad4 AFR AF: 0.0829

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.354

Alfa AF: 0.399 Hom.: 22896

Bravo AF: 0.311

Asia WGS AF: 0.241 AC: 839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.62

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: rs10489997; hg19: chr2-160405498;