chr7-73490480-C-T

Position:

• chr7-73490480-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000339594.9(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 ENST00000339594.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.694-1089G>A		intron_variant		ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.694-1089G>A		intron_variant			NP_001357331.1
BAZ1B	XM_047421016.1	c.694-1089G>A		intron_variant			XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.694-1089G>A		intron_variant		1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.694-1089G>A		intron_variant		2		ENSP00000385442.1

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

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.188

Alfa AF: 0.180 Hom.: 3338

Bravo AF: 0.210

Asia WGS AF: 0.128 AC: 444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.099
DANN	Benign	0.16

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

LitVar

Other links and lift over

dbSNP: rs17145713; hg19: chr7-72904810;