Genetic Variant BAZ1B:c.370-140C>G (chr7-73498838-G-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.370-140C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 716,862 control chromosomes in the GnomAD database, including 200,555 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 0.75 ( 42852 hom., cov: 32)

Exomes 𝑓: 0.74 ( 157703 hom. )

Consequence

BAZ1B
NM_032408.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.988

Publications

4 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	NM_032408.4	MANE Select	c.370-140C>G		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.370-140C>G		intron	N/A	NP_001357331.1	Q9UIG0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.370-140C>G		intron	N/A	ENSP00000342434.4	Q9UIG0-1
	BAZ1B	ENST00000404251.1	TSL:2	c.370-140C>G		intron	N/A	ENSP00000385442.1	Q9UIG0-1

Frequencies

GnomAD3 genomes

AF:

0.749

AC:

113839

AN:

151978

Hom.:

42827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.784

Gnomad AMI

AF:

0.673

Gnomad AMR

AF:

0.699

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.925

Gnomad SAS

AF:

0.812

Gnomad FIN

AF:

0.771

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.728

Gnomad OTH

AF:

0.722

GnomAD4 exome

AF:

0.743

AC:

419700

AN:

564766

Hom.:

157703

AF XY:

0.745

AC XY:

216939

AN XY:

291162

show subpopulations

African (AFR)

AF:

0.778

AC:

11269

AN:

14476

American (AMR)

AF:

0.689

AC:

12981

AN:

18850

Ashkenazi Jewish (ASJ)

AF:

0.599

AC:

8597

AN:

14352

East Asian (EAS)

AF:

0.946

AC:

29835

AN:

31546

South Asian (SAS)

AF:

0.796

AC:

36516

AN:

45882

European-Finnish (FIN)

AF:

0.769

AC:

24050

AN:

31290

Middle Eastern (MID)

AF:

0.688

AC:

1510

AN:

2194

European-Non Finnish (NFE)

AF:

0.726

AC:

273292

AN:

376472

Other (OTH)

AF:

0.729

AC:

21650

AN:

29704

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

5166

10332

15499

20665

25831

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3506

7012

10518

14024

17530

<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:

0.749

AC:

113921

AN:

152096

Hom.:

42852

Cov.:

AF XY:

0.750

AC XY:

55757

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.784

AC:

32534

AN:

41472

American (AMR)

AF:

0.699

AC:

10668

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2061

AN:

3464

East Asian (EAS)

AF:

0.925

AC:

4793

AN:

5184

South Asian (SAS)

AF:

0.810

AC:

3909

AN:

4824

European-Finnish (FIN)

AF:

0.771

AC:

8146

AN:

10564

Middle Eastern (MID)

AF:

0.680

AC:

200

AN:

294

European-Non Finnish (NFE)

AF:

0.728

AC:

49475

AN:

68004

Other (OTH)

AF:

0.722

AC:

1524

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1473

2946

4419

5892

7365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<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:

0.741

Hom.:

5185

Bravo

AF:

0.742

Asia WGS

AF:

0.859

AC:

2986

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.23

(source)

DANN

Benign

0.39

PhyloP100

-0.99

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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