rs7576570

Variant names:

• chr2-159347187-G-A
• rs7576570
• NM_013450.4:c.5454+299C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-159347187-G-A
• chr2-159347187-G-C
• chr2-159347187-G-T

Variant summary

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

The NM_013450.4(BAZ2B):​c.5454+299C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,178 control chromosomes in the GnomAD database, including 64,550 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 (64550 hom., cov: 30)
• Consequence: BAZ2B NM_013450.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BAZ2B	NM_013450.4	c.5454+299C>T		intron_variant	Intron 31 of 36	ENST00000392783.7	NP_038478.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BAZ2B	ENST00000392783.7	c.5454+299C>T		intron_variant	Intron 31 of 36	5	NM_013450.4	ENSP00000376534.2

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138936 AN: 152060 Hom.: 64498 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.967

Gnomad ASJ AF: 0.976

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.914 AC: 139047 AN: 152178 Hom.: 64550 Cov.: 30 AF XY: 0.916 AC XY: 68144 AN XY: 74410

African (AFR) AF: 0.734 AC: 30433 AN: 41460

American (AMR) AF: 0.967 AC: 14780 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.976 AC: 3388 AN: 3472

East Asian (EAS) AF: 0.860 AC: 4451 AN: 5176

South Asian (SAS) AF: 0.934 AC: 4506 AN: 4826

European-Finnish (FIN) AF: 0.993 AC: 10533 AN: 10604

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67774 AN: 68032

Other (OTH) AF: 0.936 AC: 1981 AN: 2116

Alfa AF: 0.970 Hom.: 83448

Bravo AF: 0.904

Asia WGS AF: 0.884 AC: 3073 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		1.1
PromoterAI		0.014	Neutral
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: rs7576570; hg19: chr2-160203698;