chr7-73498838-G-C

Position:

• chr7-73498838-G-C

Variant summary

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

The NM_032408.4(BAZ1B):​c.370-140C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 716,862 control chromosomes in the GnomAD database, including 200,555 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 0.75 (42852 hom., cov: 32)
  • Exomes 𝑓: 0.74 (157703 hom.)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

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 (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.370-140C>G		intron_variant		ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.370-140C>G		intron_variant			NP_001357331.1
BAZ1B	XM_047421016.1	c.370-140C>G		intron_variant			XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.370-140C>G		intron_variant		1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.370-140C>G		intron_variant		2		ENSP00000385442.1

Frequencies

GnomAD3 genomes AF: 0.749 AC: 113839 AN: 151978 Hom.: 42827 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.722

GnomAD4 exome AF: 0.743 AC: 419700 AN: 564766 Hom.: 157703 AF XY: 0.745 AC XY: 216939 AN XY: 291162

Gnomad4 AFR exome AF: 0.778

Gnomad4 AMR exome AF: 0.689

Gnomad4 ASJ exome AF: 0.599

Gnomad4 EAS exome AF: 0.946

Gnomad4 SAS exome AF: 0.796

Gnomad4 FIN exome AF: 0.769

Gnomad4 NFE exome AF: 0.726

Gnomad4 OTH exome AF: 0.729

GnomAD4 genome AF: 0.749 AC: 113921 AN: 152096 Hom.: 42852 Cov.: 32 AF XY: 0.750 AC XY: 55757 AN XY: 74330

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.722

Alfa AF: 0.741 Hom.: 5185

Bravo AF: 0.742

Asia WGS AF: 0.859 AC: 2986 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	0.23
DANN	Benign	0.39

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: rs2353082; hg19: chr7-72913168;