Genetic Variant BAZ2A:c.-200G>A (chr12-56636902-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000898922.1(BAZ2A):c.-200G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,446 control chromosomes in the GnomAD database, including 11,021 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 0.37 ( 10997 hom., cov: 31)

Exomes 𝑓: 0.32 ( 24 hom. )

Consequence

BAZ2A
ENST00000898922.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

Publications

15 publications found

Variant links:

COSMIC-nc: COSV51644468

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]

BAZ2A links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

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

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

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56651

AN:

151884

Hom.:

10976

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.256

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.288

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.355

Gnomad OTH

AF:

0.357

GnomAD4 exome

AF:

0.316

AC:

141

AN:

446

Hom.:

AF XY:

0.302

AC XY:

AN XY:

328

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.250

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.333

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AF:

0.625

AC:

AN:

European-Non Finnish (NFE)

AF:

0.321

AC:

118

AN:

368

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.373

AC:

56732

AN:

152000

Hom.:

10997

Cov.:

AF XY:

0.367

AC XY:

27263

AN XY:

74282

show subpopulations

African (AFR)

AF:

0.475

AC:

19698

AN:

41458

American (AMR)

AF:

0.318

AC:

4851

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.405

AC:

1405

AN:

3470

East Asian (EAS)

AF:

0.256

AC:

1320

AN:

5158

South Asian (SAS)

AF:

0.252

AC:

1215

AN:

4820

European-Finnish (FIN)

AF:

0.288

AC:

3040

AN:

10562

Middle Eastern (MID)

AF:

0.411

AC:

120

AN:

292

European-Non Finnish (NFE)

AF:

0.355

AC:

24118

AN:

67954

Other (OTH)

AF:

0.354

AC:

745

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1803

3607

5410

7214

9017

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.358

Hom.:

26829

Bravo

AF:

0.382

Asia WGS

AF:

0.256

AC:

896

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.29

(source)

DANN

Benign

0.80

PhyloP100

-1.9

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over