7-73462836-T-C

Variant names:

• chr7-73462836-T-C
• rs2074755
• NM_032408.4:c.3249+86A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032408.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	NM_032408.4	MANE Select	c.3249+86A>G		intron	N/A	NP_115784.1	Q9UIG0-1
	BAZ1B	NM_001370402.1		c.3249+86A>G		intron	N/A	NP_001357331.1	Q9UIG0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ1B	ENST00000339594.9	TSL:1 MANE Select	c.3249+86A>G		intron	N/A	ENSP00000342434.4	Q9UIG0-1
	BAZ1B	ENST00000404251.1	TSL:2	c.3249+86A>G		intron	N/A	ENSP00000385442.1	Q9UIG0-1
	BAZ1B	ENST00000466844.1	TSL:4	n.455A>G		non_coding_transcript_exon	Exon 3 of 3

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

African (AFR) AF: 0.0396 AC: 1134 AN: 28646

American (AMR) AF: 0.0595 AC: 2463 AN: 41398

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 2677 AN: 24198

East Asian (EAS) AF: 0.0990 AC: 3812 AN: 38492

South Asian (SAS) AF: 0.0962 AC: 7633 AN: 79304

European-Finnish (FIN) AF: 0.124 AC: 6563 AN: 52854

Middle Eastern (MID) AF: 0.150 AC: 767 AN: 5118

European-Non Finnish (NFE) AF: 0.122 AC: 114465 AN: 936540

Other (OTH) AF: 0.108 AC: 5806 AN: 53532

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

African (AFR) AF: 0.0419 AC: 1739 AN: 41542

American (AMR) AF: 0.0723 AC: 1105 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 379 AN: 3466

East Asian (EAS) AF: 0.101 AC: 522 AN: 5186

South Asian (SAS) AF: 0.0952 AC: 459 AN: 4822

European-Finnish (FIN) AF: 0.118 AC: 1247 AN: 10604

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8324 AN: 68006

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.0768 Hom.: 218

Bravo AF: 0.0840

Asia WGS AF: 0.0980 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.1
DANN	Benign	0.55
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2074755; hg19: chr7-72877166; COSMIC: COSV59994626;