Genetic Variant BAZ2B:c.1294-1203G>A (chr2-159434566-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_013450.4(BAZ2B):c.1294-1203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,874 control chromosomes in the GnomAD database, including 9,800 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 ( 9799 hom., cov: 32)

Exomes 𝑓: 0.50 ( 1 hom. )

Consequence

BAZ2B
NM_013450.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.317

Publications

6 publications found

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 Gene-Disease associations (from GenCC):

neurodevelopmental disorder
Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics
complex neurodevelopmental disorder
Inheritance: AD Classification: LIMITED Submitted by: ClinGen

BAZ2B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ2B	NM_013450.4 link	c.1294-1203G>A		intron_variant	Intron 8 of 36	ENST00000392783.7	NP_038478.2	Q9UIF8-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BAZ2B	ENST00000392783.7 link	c.1294-1203G>A	intron_variant	Intron 8 of 36	5	NM_013450.4	ENSP00000376534.2	Q9UIF8-1
BAZ2B	ENST00000392782.5 link	c.1288-1203G>A	intron_variant	Intron 8 of 35	1		ENSP00000376533.1	Q9UIF8-5
BAZ2B	ENST00000472953.1 link	n.988G>A	non_coding_transcript_exon_variant	Exon 1 of 8	5
BAZ2B	ENST00000718451.1 link	c.1288-1203G>A	intron_variant	Intron 8 of 36			ENSP00000520831.1

Frequencies

GnomAD3 genomes

AF:

0.324

AC:

49210

AN:

151748

Hom.:

9795

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.639

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.330

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.190

Gnomad FIN

AF:

0.338

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.456

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.324

AC:

49232

AN:

151866

Hom.:

9799

Cov.:

AF XY:

0.314

AC XY:

23290

AN XY:

74232

show subpopulations

African (AFR)

AF:

0.127

AC:

5278

AN:

41514

American (AMR)

AF:

0.296

AC:

4515

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.330

AC:

1145

AN:

3472

East Asian (EAS)

AF:

0.286

AC:

1480

AN:

5170

South Asian (SAS)

AF:

0.191

AC:

918

AN:

4814

European-Finnish (FIN)

AF:

0.338

AC:

3566

AN:

10542

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.456

AC:

30906

AN:

67806

Other (OTH)

AF:

0.345

AC:

728

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1537

3075

4612

6150

7687

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

478

956

1434

1912

2390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.374

Hom.:

1607

Bravo

AF:

0.316

Asia WGS

AF:

0.240

AC:

838

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

3.4

(source)

DANN

Benign

0.70

PhyloP100

0.32

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over