rs12692550

Variant names:

• chr2-159393260-T-C
• rs12692550
• NM_013450.4:c.3075+2509A>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.3075+2509A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,012 control chromosomes in the GnomAD database, including 37,008 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 0.66 (37008 hom., cov: 31)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 7 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

ENSG00000223642 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.3075+2509A>G		intron_variant	Intron 20 of 36	ENST00000392783.7	NP_038478.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ2B	ENST00000392783.7	c.3075+2509A>G		intron_variant	Intron 20 of 36	5	NM_013450.4	ENSP00000376534.2

Frequencies

GnomAD3 genomes AF: 0.665 AC: 100935 AN: 151894 Hom.: 37005 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.847

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.664 AC: 100954 AN: 152012 Hom.: 37008 Cov.: 31 AF XY: 0.664 AC XY: 49351 AN XY: 74290

African (AFR) AF: 0.358 AC: 14857 AN: 41446

American (AMR) AF: 0.542 AC: 8276 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2599 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3645 AN: 5156

South Asian (SAS) AF: 0.680 AC: 3276 AN: 4818

European-Finnish (FIN) AF: 0.847 AC: 8961 AN: 10574

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56949 AN: 67974

Other (OTH) AF: 0.674 AC: 1424 AN: 2112

Alfa AF: 0.775 Hom.: 43873

Bravo AF: 0.629

Asia WGS AF: 0.663 AC: 2304 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.69
DANN	Benign	0.46
PhyloP100		0.066
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: rs12692550; hg19: chr2-160249771;