rs714052

Variant names:

• chr7-73450539-A-G
• rs714052
• NM_032408.4:c.3580+308T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032408.4(BAZ1B):​c.3580+308T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,246 control chromosomes in the GnomAD database, including 787 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 (787 hom., cov: 32)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 61 publications found

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.3580+308T>C		intron_variant	Intron 14 of 19	ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.3580+308T>C		intron_variant	Intron 14 of 18		NP_001357331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.3580+308T>C		intron_variant	Intron 14 of 19	1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.3580+308T>C		intron_variant	Intron 14 of 18	2		ENSP00000385442.1

Frequencies

GnomAD3 genomes AF: 0.0925 AC: 14074 AN: 152126 Hom.: 786 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0726

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0950

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.0867

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0925 AC: 14082 AN: 152246 Hom.: 787 Cov.: 32 AF XY: 0.0923 AC XY: 6874 AN XY: 74456

African (AFR) AF: 0.0418 AC: 1739 AN: 41556

American (AMR) AF: 0.0724 AC: 1108 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 380 AN: 3472

East Asian (EAS) AF: 0.101 AC: 524 AN: 5172

South Asian (SAS) AF: 0.0953 AC: 460 AN: 4828

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8332 AN: 67998

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.107 Hom.: 1500

Bravo AF: 0.0841

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	-0.87
CADD	Benign	2.4
DANN	Benign	0.51
PhyloP100		-0.53
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs714052; hg19: chr7-72864869;