rs714052

Positions:

• chr7-73450539-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• 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/exons	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.3580+308T>C		intron_variant		ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.3580+308T>C		intron_variant			NP_001357331.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.3580+308T>C		intron_variant		1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.3580+308T>C		intron_variant		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

Gnomad4 AFR AF: 0.0418

Gnomad4 AMR AF: 0.0724

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0953

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.123

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.111 Hom.: 308

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

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: rs714052; hg19: chr7-72864869;