rs17400042

Variant names:

• chr7-73482220-A-G
• rs17400042
• NM_032408.4:c.892-3651T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_032408.4(BAZ1B):​c.892-3651T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 152,324 control chromosomes in the GnomAD database, including 44 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 0.021 (44 hom., cov: 32)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 6 publications found

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]

BAZ1B Gene-Disease associations (from GenCC):

• autism spectrum disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0208 (3168/152324) while in subpopulation NFE AF = 0.0307 (2091/68020). AF 95% confidence interval is 0.0296. There are 44 homozygotes in GnomAd4. There are 1574 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High AC in GnomAd4 at 3168 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.892-3651T>C		intron_variant	Intron 6 of 19	ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.892-3651T>C		intron_variant	Intron 6 of 18		NP_001357331.1
BAZ1B	XM_047421016.1	c.892-3651T>C		intron_variant	Intron 6 of 12		XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.892-3651T>C		intron_variant	Intron 6 of 19	1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.892-3651T>C		intron_variant	Intron 6 of 18	2		ENSP00000385442.1

Frequencies

GnomAD3 genomes AF: 0.0208 AC: 3168 AN: 152206 Hom.: 45 Cov.: 32

Gnomad AFR AF: 0.00454

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0308

Gnomad OTH AF: 0.0258

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0208 AC: 3168 AN: 152324 Hom.: 44 Cov.: 32 AF XY: 0.0211 AC XY: 1574 AN XY: 74486

African (AFR) AF: 0.00452 AC: 188 AN: 41570

American (AMR) AF: 0.0157 AC: 240 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0259 AC: 125 AN: 4832

European-Finnish (FIN) AF: 0.0327 AC: 347 AN: 10616

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2091 AN: 68020

Other (OTH) AF: 0.0246 AC: 52 AN: 2116

Alfa AF: 0.0276 Hom.: 43

Bravo AF: 0.0177

Asia WGS AF: 0.00895 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.4
DANN	Benign	0.59
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs17400042; hg19: chr7-72896550;