rs941207

Variant names:

• chr12-56629500-C-A
• rs941207
• NM_001300905.2:c.-3+625G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-56629500-C-A
• chr12-56629500-C-G

Variant summary

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

The NM_001300905.2(BAZ2A):​c.-3+625G>T variant causes a intron 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 NM_001300905.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 26 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: NM_001300905.2. 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
	BAZ2A	NM_001300905.2	MANE Select	c.-3+625G>T		intron	N/A	NP_001287834.1	F8VU39
	BAZ2A	NM_013449.4		c.4+6682G>T		intron	N/A	NP_038477.2	Q9UIF9-1
	BAZ2A	NM_001351156.2		c.-3+1276G>T		intron	N/A	NP_001338085.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BAZ2A	ENST00000549884.6	TSL:2 MANE Select	c.-3+625G>T		intron	N/A	ENSP00000447941.1	F8VU39
	BAZ2A	ENST00000551812.5	TSL:1	c.4+6682G>T		intron	N/A	ENSP00000446880.1	Q9UIF9-1
	BAZ2A	ENST00000379441.7	TSL:1	c.4+6682G>T		intron	N/A	ENSP00000368754.3	J3KPG5

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.80
PhyloP100		-0.083

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: rs941207; hg19: chr12-57023284;