rs2240466

chr7-73441939-G-A

Variant summary

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

The NM_032408.4(BAZ1B):c.*15+242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 497,894 control chromosomes in the GnomAD database, including 3,012 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 (781 hom., cov: 32)
  • Exomes 𝑓: 0.11 (2231 hom.)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.36

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=-0.89).
• 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.*15+242C>T		intron_variant		ENST00000339594.9
BAZ1B	NM_001370402.1	c.*257C>T		3_prime_UTR_variant	19/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ1B	ENST00000339594.9	c.*15+242C>T		intron_variant		1	NM_032408.4	P1
BAZ1B	ENST00000404251.1	c.*257C>T		3_prime_UTR_variant	19/19	2		P1

Frequencies

GnomAD3 genomes AF: 0.0923 AC: 14044 AN: 152074 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0420

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0859

GnomAD4 exome AF: 0.108 AC: 37367 AN: 345702 Hom.: 2231 Cov.: 0 AF XY: 0.109 AC XY: 19464 AN XY: 179304

Gnomad4 AFR exome AF: 0.0379

Gnomad4 AMR exome AF: 0.0638

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.0996

Gnomad4 SAS exome AF: 0.0938

Gnomad4 FIN exome AF: 0.123

Gnomad4 NFE exome AF: 0.115

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.0923 AC: 14052 AN: 152192 Hom.: 781 Cov.: 32 AF XY: 0.0921 AC XY: 6855 AN XY: 74406

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.0721

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0995

Gnomad4 SAS AF: 0.0950

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0897

Alfa AF: 0.110 Hom.: 1444

Bravo AF: 0.0839

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	-0.89
Cadd	Benign	0.16
Dann	Benign	0.62

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: rs2240466; hg19: chr7-72856269;