Genetic Variant BAZ1B:c.*15+81A>G (chr7-73442100-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_032408.4(BAZ1B):c.*15+81A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 960,804 control chromosomes in the GnomAD database, including 15,130 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 0.21 ( 3701 hom., cov: 30)

Exomes 𝑓: 0.15 ( 11429 hom. )

Consequence

BAZ1B
NM_032408.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45

Publications

52 publications found

Variant links:

Genes affected

BAZ1B (HGNC:961): (bromodomain adjacent to zinc finger domain 1B) This gene encodes a member of the bromodomain protein family. The bromodomain is a structural motif characteristic of proteins involved in chromatin-dependent regulation of transcription. This gene is deleted in Williams-Beuren syndrome, a developmental disorder caused by deletion of multiple genes at 7q11.23. [provided by RefSeq, Jul 2008]

BAZ1B Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

BAZ1B links:

Genome browser will be placed here

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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032408.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	NM_032408.4	MANE Select	c.*15+81A>G		intron	N/A	NP_115784.1
	BAZ1B	NM_001370402.1		c.*96A>G		3_prime_UTR	Exon 19 of 19	NP_001357331.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.*15+81A>G		intron	N/A	ENSP00000342434.4
	BAZ1B	ENST00000404251.1	TSL:2	c.*96A>G		3_prime_UTR	Exon 19 of 19	ENSP00000385442.1

Frequencies

GnomAD3 genomes

AF:

0.206

AC:

31256

AN:

151626

Hom.:

3679

Cov.:

show subpopulations

Gnomad AFR

AF:

0.303

Gnomad AMI

AF:

0.152

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.160

Gnomad EAS

AF:

0.0971

Gnomad SAS

AF:

0.109

Gnomad FIN

AF:

0.154

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.185

GnomAD4 exome

AF:

0.148

AC:

119774

AN:

809060

Hom.:

11429

Cov.:

AF XY:

0.147

AC XY:

60718

AN XY:

414360

show subpopulations

African (AFR)

AF:

0.275

AC:

5247

AN:

19086

American (AMR)

AF:

0.103

AC:

2915

AN:

28422

Ashkenazi Jewish (ASJ)

AF:

0.145

AC:

2372

AN:

16364

East Asian (EAS)

AF:

0.0901

AC:

3243

AN:

36012

South Asian (SAS)

AF:

0.104

AC:

6181

AN:

59248

European-Finnish (FIN)

AF:

0.166

AC:

5664

AN:

34194

Middle Eastern (MID)

AF:

0.141

AC:

376

AN:

2664

European-Non Finnish (NFE)

AF:

0.153

AC:

87961

AN:

575150

Other (OTH)

AF:

0.153

AC:

5815

AN:

37920

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

5018

10036

15053

20071

25089

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1958

3916

5874

7832

9790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.206

AC:

31326

AN:

151744

Hom.:

3701

Cov.:

AF XY:

0.203

AC XY:

15028

AN XY:

74170

show subpopulations

African (AFR)

AF:

0.304

AC:

12560

AN:

41288

American (AMR)

AF:

0.138

AC:

2106

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.160

AC:

555

AN:

3466

East Asian (EAS)

AF:

0.0976

AC:

503

AN:

5156

South Asian (SAS)

AF:

0.110

AC:

529

AN:

4820

European-Finnish (FIN)

AF:

0.154

AC:

1621

AN:

10518

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.189

AC:

12866

AN:

67936

Other (OTH)

AF:

0.188

AC:

396

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1189

2378

3566

4755

5944

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

312

624

936

1248

1560

<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:

0.191

Hom.:

7963

Bravo

AF:

0.210

Asia WGS

AF:

0.130

AC:

454

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.030

(source)

DANN

Benign

0.46

PhyloP100

-2.5

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over