rs12056034

chr7-73464315-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.3071+1124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0997 in 191,628 control chromosomes in the GnomAD database, including 1,166 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 (783 hom., cov: 32)
  • Exomes 𝑓: 0.13 (383 hom.)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.920

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=-0.9).
• 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	UniProt
BAZ1B	NM_032408.4	c.3071+1124T>C		intron_variant		ENST00000339594.9
BAZ1B	NM_001370402.1	c.3071+1124T>C		intron_variant
BAZ1B	XM_047421016.1	c.3072-119T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ1B	ENST00000339594.9	c.3071+1124T>C		intron_variant		1	NM_032408.4	P1
BAZ1B	ENST00000404251.1	c.3071+1124T>C		intron_variant		2		P1
BAZ1B	ENST00000466844.1	n.191+1124T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14058 AN: 152184 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0724

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0866

GnomAD4 exome AF: 0.128 AC: 5036 AN: 39324 Hom.: 383 AF XY: 0.129 AC XY: 2462 AN XY: 19148

Gnomad4 AFR exome AF: 0.0334

Gnomad4 AMR exome AF: 0.0192

Gnomad4 ASJ exome AF: 0.128

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.131

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.0924 AC: 14066 AN: 152304 Hom.: 783 Cov.: 32 AF XY: 0.0922 AC XY: 6864 AN XY: 74470

Gnomad4 AFR AF: 0.0417

Gnomad4 AMR AF: 0.0722

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.0949

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0904

Alfa AF: 0.110 Hom.: 141

Bravo AF: 0.0840

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	-0.90
Cadd	Benign	4.3
Dann	Benign	0.54

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: rs12056034; hg19: chr7-72878645;