Genetic Variant BAZ1B:c.3249+86A>G (chr7-73462836-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.3249+86A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,412,314 control chromosomes in the GnomAD database, including 9,726 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 0.092 ( 783 hom., cov: 32)

Exomes 𝑓: 0.12 ( 8943 hom. )

Consequence

BAZ1B
NM_032408.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.658

Publications

24 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 (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4 link	c.3249+86A>G	intron_variant	Intron 12 of 19	ENST00000339594.9	NP_115784.1	Q9UIG0-1
BAZ1B	NM_001370402.1 link	c.3249+86A>G	intron_variant	Intron 12 of 18		NP_001357331.1
BAZ1B	XM_047421016.1 link	c.*232A>G	downstream_gene_variant			XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BAZ1B	ENST00000339594.9 link	c.3249+86A>G	intron_variant	Intron 12 of 19	1	NM_032408.4	ENSP00000342434.4	Q9UIG0-1
BAZ1B	ENST00000466844.1 link	n.455A>G	non_coding_transcript_exon_variant	Exon 3 of 3	4
BAZ1B	ENST00000404251.1 link	c.3249+86A>G	intron_variant	Intron 12 of 18	2		ENSP00000385442.1	Q9UIG0-1

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14053

AN:

152114

Hom.:

782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0420

Gnomad AMI

AF:

0.0637

Gnomad AMR

AF:

0.0725

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.100

Gnomad SAS

AF:

0.0949

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.0861

GnomAD4 exome

AF:

0.115

AC:

145320

AN:

1260082

Hom.:

8943

Cov.:

AF XY:

0.115

AC XY:

73094

AN XY:

635618

show subpopulations

African (AFR)

AF:

0.0396

AC:

1134

AN:

28646

American (AMR)

AF:

0.0595

AC:

2463

AN:

41398

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

2677

AN:

24198

East Asian (EAS)

AF:

0.0990

AC:

3812

AN:

38492

South Asian (SAS)

AF:

0.0962

AC:

7633

AN:

79304

European-Finnish (FIN)

AF:

0.124

AC:

6563

AN:

52854

Middle Eastern (MID)

AF:

0.150

AC:

767

AN:

5118

European-Non Finnish (NFE)

AF:

0.122

AC:

114465

AN:

936540

Other (OTH)

AF:

0.108

AC:

5806

AN:

53532

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

6222

12444

18666

24888

31110

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3852

7704

11556

15408

19260

<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:

0.0924

AC:

14061

AN:

152232

Hom.:

783

Cov.:

AF XY:

0.0922

AC XY:

6865

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.0419

AC:

1739

AN:

41542

American (AMR)

AF:

0.0723

AC:

1105

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

379

AN:

3466

East Asian (EAS)

AF:

0.101

AC:

522

AN:

5186

South Asian (SAS)

AF:

0.0952

AC:

459

AN:

4822

European-Finnish (FIN)

AF:

0.118

AC:

1247

AN:

10604

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8324

AN:

68006

Other (OTH)

AF:

0.0900

AC:

190

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

646

1292

1937

2583

3229

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

312

468

624

780

<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:

0.0768

Hom.:

218

Bravo

AF:

0.0840

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.1

(source)

DANN

Benign

0.55

PhyloP100

0.66

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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