Genetic Variant NM_032408.4:c.3071+1124T>C (chr7-73464315-A-G) – 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.3071+1124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 191,628 control chromosomes in the GnomAD database, including 1,166 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: 0.13 ( 383 hom. )

Consequence

BAZ1B
NM_032408.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.920

Publications

17 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=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 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.3071+1124T>C		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.3071+1124T>C		intron	N/A	NP_001357331.1	Q9UIG0-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.3071+1124T>C	intron	N/A	ENSP00000342434.4	Q9UIG0-1
BAZ1B	ENST00000404251.1	TSL:2	c.3071+1124T>C	intron	N/A	ENSP00000385442.1	Q9UIG0-1
BAZ1B	ENST00000466844.1	TSL:4	n.191+1124T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0924

AC:

14058

AN:

152184

Hom.:

782

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0419

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0724

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.101

Gnomad SAS

AF:

0.0946

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.0866

GnomAD4 exome

AF:

0.128

AC:

5036

AN:

39324

Hom.:

383

AF XY:

0.129

AC XY:

2462

AN XY:

19148

show subpopulations

African (AFR)

AF:

0.0334

AC:

AN:

688

American (AMR)

AF:

0.0192

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.128

AC:

AN:

234

East Asian (EAS)

AF:

0.101

AC:

AN:

168

South Asian (SAS)

AF:

0.105

AC:

AN:

704

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.100

AC:

AN:

European-Non Finnish (NFE)

AF:

0.131

AC:

4742

AN:

36094

Other (OTH)

AF:

0.109

AC:

140

AN:

1288

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

235

469

704

938

1173

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

236

472

708

944

1180

<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:

14066

AN:

152304

Hom.:

783

Cov.:

AF XY:

0.0922

AC XY:

6864

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0417

AC:

1735

AN:

41570

American (AMR)

AF:

0.0722

AC:

1104

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.109

AC:

379

AN:

3468

East Asian (EAS)

AF:

0.102

AC:

527

AN:

5188

South Asian (SAS)

AF:

0.0949

AC:

458

AN:

4826

European-Finnish (FIN)

AF:

0.118

AC:

1250

AN:

10614

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8326

AN:

68028

Other (OTH)

AF:

0.0904

AC:

191

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

631

1262

1892

2523

3154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

158

316

474

632

790

<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:

0.108

Hom.:

142

Bravo

AF:

0.0840

Asia WGS

AF:

0.0980

AC:

342

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

4.3

(source)

DANN

Benign

0.54

PhyloP100

0.92

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