chr2-159322264-C-T

Position:

• chr2-159322264-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.6354-1846G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,974 control chromosomes in the GnomAD database, including 27,443 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 0.59 (27443 hom., cov: 32)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAZ2B	NM_013450.4	c.6354-1846G>A		intron_variant		ENST00000392783.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ2B	ENST00000392783.7	c.6354-1846G>A		intron_variant		5	NM_013450.4	P1
BAZ2B	ENST00000392782.5	c.6246-1846G>A		intron_variant		1
BAZ2B	ENST00000548440.1	n.868-237G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89008 AN: 151856 Hom.: 27400 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.586 AC: 89102 AN: 151974 Hom.: 27443 Cov.: 32 AF XY: 0.600 AC XY: 44597 AN XY: 74268

Gnomad4 AFR AF: 0.696

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.581

Alfa AF: 0.525 Hom.: 2704

Bravo AF: 0.597

Asia WGS AF: 0.857 AC: 2975 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	0.63
DANN	Benign	0.52

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: rs174226; hg19: chr2-160178775;