7-73490480-C-T

Variant names:

• chr7-73490480-C-T
• rs17145713
• NM_032408.4:c.694-1089G>A

Variant summary

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

The NM_032408.4(BAZ1B):​c.694-1089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 152,062 control chromosomes in the GnomAD database, including 3,726 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 0.21 (3726 hom., cov: 32)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 43 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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.694-1089G>A		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.694-1089G>A		intron	N/A	NP_001357331.1	Q9UIG0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.694-1089G>A		intron	N/A	ENSP00000342434.4	Q9UIG0-1
	BAZ1B	ENST00000404251.1	TSL:2	c.694-1089G>A		intron	N/A	ENSP00000385442.1	Q9UIG0-1

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31486 AN: 151942 Hom.: 3704 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.208 AC: 31555 AN: 152062 Hom.: 3726 Cov.: 32 AF XY: 0.204 AC XY: 15157 AN XY: 74324

African (AFR) AF: 0.306 AC: 12681 AN: 41470

American (AMR) AF: 0.140 AC: 2134 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3468

East Asian (EAS) AF: 0.101 AC: 521 AN: 5176

South Asian (SAS) AF: 0.110 AC: 532 AN: 4824

European-Finnish (FIN) AF: 0.157 AC: 1661 AN: 10552

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12883 AN: 67984

Other (OTH) AF: 0.188 AC: 397 AN: 2112

Alfa AF: 0.189 Hom.: 9815

Bravo AF: 0.210

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.099
DANN	Benign	0.16
PhyloP100		-1.6
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: rs17145713; hg19: chr7-72904810;