Variant chr2-159325791-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_013450.4(BAZ2B):c.6071G>A(p.Ser2024Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 1,606,358 control chromosomes in the GnomAD database, including 41,452 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.24 ( 4439 hom., cov: 32)

Exomes 𝑓: 0.22 ( 37013 hom. )

Consequence

BAZ2B
NM_013450.4 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.02

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001219511).

BP6

Variant 2-159325791-C-T is Benign according to our data. Variant chr2-159325791-C-T is described in ClinVar as [Benign]. Clinvar id is 3056167.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAZ2B	NM_013450.4 linkuse as main transcript	c.6071G>A	p.Ser2024Asn	missense_variant	35/37	ENST00000392783.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ2B	ENST00000392783.7 linkuse as main transcript	c.6071G>A	p.Ser2024Asn	missense_variant	35/37	5	NM_013450.4	P1	Q9UIF8-1
BAZ2B	ENST00000392782.5 linkuse as main transcript	c.5963G>A	p.Ser1988Asn	missense_variant	34/36	1			Q9UIF8-5
BAZ2B	ENST00000474437.1 linkuse as main transcript	n.611G>A		non_coding_transcript_exon_variant	4/4	3
BAZ2B	ENST00000548440.1 linkuse as main transcript	n.585G>A		non_coding_transcript_exon_variant	2/4	3

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36256

AN:

151818

Hom.:

4432

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.186

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.268

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.251

GnomAD3 exomes

AF:

0.222

AC:

54118

AN:

243724

Hom.:

6255

AF XY:

0.226

AC XY:

29856

AN XY:

132206

show subpopulations

Gnomad AFR exome

AF:

0.290

Gnomad AMR exome

AF:

0.162

Gnomad ASJ exome

AF:

0.233

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.258

Gnomad FIN exome

AF:

0.233

Gnomad NFE exome

AF:

0.222

Gnomad OTH exome

AF:

0.228

GnomAD4 exome

AF:

0.223

AC:

324086

AN:

1454422

Hom.:

37013

Cov.:

AF XY:

0.224

AC XY:

161927

AN XY:

723164

show subpopulations

Gnomad4 AFR exome

AF:

0.294

Gnomad4 AMR exome

AF:

0.169

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.171

Gnomad4 SAS exome

AF:

0.263

Gnomad4 FIN exome

AF:

0.228

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.234

GnomAD4 genome

AF:

0.239

AC:

36297

AN:

151936

Hom.:

4439

Cov.:

AF XY:

0.240

AC XY:

17855

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.196

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.267

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.218

Gnomad4 OTH

AF:

0.251

Alfa

AF:

0.225

Hom.:

8918

Bravo

AF:

0.237

TwinsUK

AF:

0.230

AC:

853

ALSPAC

AF:

0.213

AC:

821

ESP6500AA

AF:

0.284

AC:

1037

ESP6500EA

AF:

0.219

AC:

1786

ExAC

AF:

0.230

AC:

27834

Asia WGS

AF:

0.247

AC:

858

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

BAZ2B-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.60

BayesDel_noAF

Benign

-0.49

CADD

Benign

DANN

Benign

0.95

DEOGEN2

Benign

0.019

.;T

Eigen

Benign

0.11

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.89

D;D

MetaRNN

Benign

0.0012

T;T

MetaSVM

Benign

-0.96

MutationAssessor

Uncertain

2.0

.;M

MutationTaster

Benign

0.047

P;P;P;P

PrimateAI

Benign

0.46

PROVEAN

Benign

-1.2

N;N

REVEL

Benign

0.075

Sift

Benign

0.090

T;T

Sift4G

Benign

0.20

T;T

Polyphen

0.76

P;B

Vest4

0.093

MPC

0.038

ClinPred

0.011

GERP RS

5.8

Varity_R

0.091

gMVP

0.31

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over