2-159318799-T-C

Position:

• chr2-159318799-T-C

Variant summary

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

The XM_047444037.1(BAZ2B):​c.6654+1475A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 152,140 control chromosomes in the GnomAD database, including 61,337 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 0.89 (61337 hom., cov: 31)
• Consequence: BAZ2B XM_047444037.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

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=-0.9).
• 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	XM_047444037.1	c.6654+1475A>G		intron_variant			XP_047299993.1
BAZ2B	XM_005246488.3	c.6636+1475A>G		intron_variant			XP_005246545.2
BAZ2B	XM_005246489.5	c.6636+1475A>G		intron_variant			XP_005246546.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134683 AN: 152022 Hom.: 61288 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.959

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: 0.916

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

GnomAD4 genome AF: 0.886 AC: 134785 AN: 152140 Hom.: 61337 Cov.: 31 AF XY: 0.889 AC XY: 66105 AN XY: 74378

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.959

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.980

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.915

Alfa AF: 0.968 Hom.: 65066

Bravo AF: 0.874

Asia WGS AF: 0.882 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs174230; hg19: chr2-160175310;