chr2-159333698-A-C

Variant names:

• chr2-159333698-A-C
• rs4665058
• NM_013450.4:c.5797-1012T>G

Variant summary

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

The NM_013450.4(BAZ2B):​c.5797-1012T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,102 control chromosomes in the GnomAD database, including 63,584 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 0.91 (63584 hom., cov: 32)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757
• Publications: 28 publications found

Genes affected

BAZ2B (HGNC:963): (bromodomain adjacent to zinc finger domain 2B) This gene belongs to the bromodomain gene family. Members of this gene family encode proteins that are integral components of chromatin remodeling complexes. The encoded protein showed strong preference for the activating H3K14Ac mark in a histone peptide screen, suggesting a potential role in transcriptional activation. This gene may be associated with susceptibility to sudden cardiac death (SCD). [provided by RefSeq, Aug 2016]

BAZ2B Gene-Disease associations (from GenCC):

• neurodevelopmental disorder

  Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_013450.4. 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
	BAZ2B	NM_013450.4	MANE Select	c.5797-1012T>G		intron	N/A	NP_038478.2	Q9UIF8-1
	BAZ2B	NM_001329857.2		c.5740-1012T>G		intron	N/A	NP_001316786.1
	BAZ2B	NM_001329858.2		c.5722-1012T>G		intron	N/A	NP_001316787.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ2B	ENST00000392783.7	TSL:5 MANE Select	c.5797-1012T>G		intron	N/A	ENSP00000376534.2	Q9UIF8-1
	BAZ2B	ENST00000392782.5	TSL:1	c.5689-1012T>G		intron	N/A	ENSP00000376533.1	Q9UIF8-5
	BAZ2B	ENST00000911534.1		c.5797-1012T>G		intron	N/A	ENSP00000581593.1

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137862 AN: 151984 Hom.: 63527 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.980

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.907 AC: 137975 AN: 152102 Hom.: 63584 Cov.: 32 AF XY: 0.909 AC XY: 67612 AN XY: 74374

African (AFR) AF: 0.726 AC: 30107 AN: 41454

American (AMR) AF: 0.967 AC: 14782 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3430 AN: 3472

East Asian (EAS) AF: 0.868 AC: 4507 AN: 5190

South Asian (SAS) AF: 0.933 AC: 4503 AN: 4824

European-Finnish (FIN) AF: 0.980 AC: 10396 AN: 10604

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.988 AC: 67146 AN: 67956

Other (OTH) AF: 0.938 AC: 1975 AN: 2106

Alfa AF: 0.961 Hom.: 185043

Bravo AF: 0.898

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.9
DANN	Benign	0.67
PhyloP100		0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs4665058; hg19: chr2-160190209;