rs1178979

Positions:

• chr7-73442100-T-C

Variant summary

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

The NM_001370402.1(BAZ1B):​c.*96A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 960,804 control chromosomes in the GnomAD database, including 15,130 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 (3701 hom., cov: 30)
  • Exomes 𝑓: 0.15 (11429 hom.)
• Consequence: BAZ1B NM_001370402.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.*15+81A>G		intron_variant		ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.*96A>G		3_prime_UTR_variant	19/19		NP_001357331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.*15+81A>G		intron_variant		1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251	c.*96A>G		3_prime_UTR_variant	19/19	2		ENSP00000385442.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31256 AN: 151626 Hom.: 3679 Cov.: 30

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0971

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.185

GnomAD4 exome AF: 0.148 AC: 119774 AN: 809060 Hom.: 11429 Cov.: 11 AF XY: 0.147 AC XY: 60718 AN XY: 414360

Gnomad4 AFR exome AF: 0.275

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.145

Gnomad4 EAS exome AF: 0.0901

Gnomad4 SAS exome AF: 0.104

Gnomad4 FIN exome AF: 0.166

Gnomad4 NFE exome AF: 0.153

Gnomad4 OTH exome AF: 0.153

GnomAD4 genome AF: 0.206 AC: 31326 AN: 151744 Hom.: 3701 Cov.: 30 AF XY: 0.203 AC XY: 15028 AN XY: 74170

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.188

Alfa AF: 0.184 Hom.: 4183

Bravo AF: 0.210

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.030
DANN	Benign	0.46
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

LitVar

Other links and lift over

dbSNP: rs1178979; hg19: chr7-72856430;