12-56629500-C-G

Position:

• chr12-56629500-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300905.2(BAZ2A):​c.-3+625G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 152,108 control chromosomes in the GnomAD database, including 3,631 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 0.20 (3631 hom., cov: 31)
• Consequence: BAZ2A NM_001300905.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

Genes affected

BAZ2A (HGNC:962): (bromodomain adjacent to zinc finger domain 2A) Enables histone binding activity. Contributes to RNA polymerase I core promoter sequence-specific DNA binding activity. Predicted to be involved in DNA methylation; histone deacetylation; and negative regulation of macromolecule metabolic process. Predicted to act upstream of or within chromatin organization and histone modification. Located in cytosol and nuclear speck. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAZ2A	NM_001300905.2	c.-3+625G>C		intron_variant		ENST00000549884.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAZ2A	ENST00000549884.6	c.-3+625G>C		intron_variant		2	NM_001300905.2	A2

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31086 AN: 151990 Hom.: 3631 Cov.: 31

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.204 AC: 31087 AN: 152108 Hom.: 3631 Cov.: 31 AF XY: 0.202 AC XY: 15012 AN XY: 74334

Gnomad4 AFR AF: 0.0892

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.217

Alfa AF: 0.254 Hom.: 2841

Bravo AF: 0.203

Asia WGS AF: 0.194 AC: 676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs941207; hg19: chr12-57023284;