NM_032408.4:c.107+1647T>C

Variant names:

• chr7-73520180-A-G
• rs7811265
• NM_032408.4:c.107+1647T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032408.4(BAZ1B):​c.107+1647T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 148,372 control chromosomes in the GnomAD database, including 4,323 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 0.22 (4323 hom., cov: 27)
• Consequence: BAZ1B NM_032408.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.17
• Publications: 26 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ1B	NM_032408.4	c.107+1647T>C		intron_variant	Intron 1 of 19	ENST00000339594.9	NP_115784.1
BAZ1B	NM_001370402.1	c.107+1647T>C		intron_variant	Intron 1 of 18		NP_001357331.1
BAZ1B	XM_047421016.1	c.107+1647T>C		intron_variant	Intron 1 of 12		XP_047276972.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ1B	ENST00000339594.9	c.107+1647T>C		intron_variant	Intron 1 of 19	1	NM_032408.4	ENSP00000342434.4
BAZ1B	ENST00000404251.1	c.107+1647T>C		intron_variant	Intron 1 of 18	2		ENSP00000385442.1

Frequencies

GnomAD3 genomes AF: 0.222 AC: 32890 AN: 148280 Hom.: 4295 Cov.: 27

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0968

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.189

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.222 AC: 32967 AN: 148372 Hom.: 4323 Cov.: 27 AF XY: 0.218 AC XY: 15760 AN XY: 72170

African (AFR) AF: 0.358 AC: 14321 AN: 40046

American (AMR) AF: 0.147 AC: 2141 AN: 14522

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 555 AN: 3446

East Asian (EAS) AF: 0.0973 AC: 487 AN: 5006

South Asian (SAS) AF: 0.111 AC: 519 AN: 4670

European-Finnish (FIN) AF: 0.157 AC: 1580 AN: 10052

Middle Eastern (MID) AF: 0.176 AC: 49 AN: 278

European-Non Finnish (NFE) AF: 0.190 AC: 12785 AN: 67394

Other (OTH) AF: 0.191 AC: 393 AN: 2056

Alfa AF: 0.214 Hom.: 526

Bravo AF: 0.226

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.20
PhyloP100		-2.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs7811265; hg19: chr7-72934510;