12-56636902-C-A

Variant names:

• chr12-56636902-C-A
• rs1107479
• ENST00000898922.1:c.-200G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000898922.1(BAZ2A):​c.-200G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: BAZ2A ENST00000898922.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 15 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000898922.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ2A	ENST00000898922.1		c.-200G>T		5_prime_UTR_premature_start_codon_gain	Exon 1 of 30	ENSP00000568981.1
	BAZ2A	ENST00000898922.1		c.-200G>T		5_prime_UTR	Exon 1 of 30	ENSP00000568981.1
	BAZ2A	ENST00000550730.1	TSL:4	n.-86G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 26829

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.21
DANN	Benign	0.76
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1107479; hg19: chr12-57030686;