2-159467373-C-T

Variant names:

• chr2-159467373-C-T
• rs964176
• NM_013450.4:c.145+11202G>A

Variant summary

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

The NM_013450.4(BAZ2B):​c.145+11202G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,042 control chromosomes in the GnomAD database, including 10,479 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 0.33 (10479 hom., cov: 32)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.145+11202G>A		intron_variant	Intron 3 of 36	ENST00000392783.7	NP_038478.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ2B	ENST00000392783.7	c.145+11202G>A		intron_variant	Intron 3 of 36	5	NM_013450.4	ENSP00000376534.2

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50196 AN: 151922 Hom.: 10477 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.330 AC: 50203 AN: 152042 Hom.: 10479 Cov.: 32 AF XY: 0.323 AC XY: 24032 AN XY: 74328

African (AFR) AF: 0.0879 AC: 3647 AN: 41504

American (AMR) AF: 0.301 AC: 4603 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1194 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1429 AN: 5154

South Asian (SAS) AF: 0.175 AC: 846 AN: 4822

European-Finnish (FIN) AF: 0.439 AC: 4633 AN: 10552

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32492 AN: 67940

Other (OTH) AF: 0.347 AC: 733 AN: 2112

Alfa AF: 0.421 Hom.: 30661

Bravo AF: 0.315

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.59
DANN	Benign	0.59
PhyloP100		-0.90
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: rs964176; hg19: chr2-160323884;