Genetic Variant BAZ1B:c.*15+81A>T (chr7-73442100-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_032408.4(BAZ1B):c.*15+81A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

BAZ1B
NM_032408.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.45

Publications

0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4 link	c.*15+81A>T		intron_variant	Intron 19 of 19	ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1 link	c.*96A>T		3_prime_UTR_variant	Exon 19 of 19		NP_001357331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9 link	c.*15+81A>T		intron_variant	Intron 19 of 19	1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1 link	c.*96A>T		3_prime_UTR_variant	Exon 19 of 19	2		ENSP00000385442.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

810024

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

414824

African (AFR)

AF:

0.00

AC:

AN:

19112

American (AMR)

AF:

0.00

AC:

AN:

28440

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

16386

East Asian (EAS)

AF:

0.00

AC:

AN:

36040

South Asian (SAS)

AF:

0.00

AC:

AN:

59286

European-Finnish (FIN)

AF:

0.00

AC:

AN:

34222

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2666

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

575908

Other (OTH)

AF:

0.00

AC:

AN:

37964

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.026

(source)

DANN

Benign

0.65

PhyloP100

-2.5

RBP_binding_hub_radar

1.1

RBP_regulation_power_radar

2.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over