rs2074755

chr7-73462836-T-Cchr7-73462836-T-G

Variant summary

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

The NM_032408.4(BAZ1B):c.3249+86A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 1,412,314 control chromosomes in the GnomAD database, including 9,726 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 0.092 (783 hom., cov: 32)
  • Exomes 𝑓: 0.12 (8943 hom.)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

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 (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.3249+86A>G		intron_variant		ENST00000339594.9
BAZ1B	NM_001370402.1	c.3249+86A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ1B	ENST00000339594.9	c.3249+86A>G		intron_variant		1	NM_032408.4	P1
BAZ1B	ENST00000404251.1	c.3249+86A>G		intron_variant		2		P1
BAZ1B	ENST00000466844.1	n.455A>G		non_coding_transcript_exon_variant	3/3	4

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14053 AN: 152114 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0861

GnomAD4 exome AF: 0.115 AC: 145320 AN: 1260082 Hom.: 8943 Cov.: 18 AF XY: 0.115 AC XY: 73094 AN XY: 635618

Gnomad4 AFR exome AF: 0.0396

Gnomad4 AMR exome AF: 0.0595

Gnomad4 ASJ exome AF: 0.111

Gnomad4 EAS exome AF: 0.0990

Gnomad4 SAS exome AF: 0.0962

Gnomad4 FIN exome AF: 0.124

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.108

GnomAD4 genome AF: 0.0924 AC: 14061 AN: 152232 Hom.: 783 Cov.: 32 AF XY: 0.0922 AC XY: 6865 AN XY: 74446

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0678 Hom.: 104

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	-0.85
Cadd	Benign	7.1
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs2074755; hg19: chr7-72877166; COSMIC: COSV59994626;