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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4 link	c.370-140C>G	intron_variant	Intron 3 of 19	ENST00000339594.9	NP_115784.1	Q9UIG0-1
BAZ1B	NM_001370402.1 link	c.370-140C>G	intron_variant	Intron 3 of 18		NP_001357331.1
BAZ1B	XM_047421016.1 link	c.370-140C>G	intron_variant	Intron 3 of 12		XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9 link	c.370-140C>G		intron_variant	Intron 3 of 19	1	NM_032408.4	ENSP00000342434.4		Q9UIG0-1
BAZ1B	ENST00000404251.1 link	c.370-140C>G		intron_variant	Intron 3 of 18	2		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 v4.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over