Genetic Variant CSNK2A2:c.*18-2669G>A (chr16-58161022-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 NM_001896.4(CSNK2A2):c.*18-2669G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,018 control chromosomes in the GnomAD database, including 11,035 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 ( 11031 hom., cov: 31)

Exomes 𝑓: 0.50 ( 4 hom. )

Consequence

CSNK2A2
NM_001896.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.133

Publications

13 publications found

Variant links:

Genes affected

CSNK2A2 (HGNC:2459): (casein kinase 2 alpha 2) This gene encodes the alpha', or alpha 2, catalytic subunit of the protein kinase enzyme, casein kinase 2 (CK2). Casein kinase 2 is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythms. This heterotetrameric kinase includes two catalytic subunits, either alpha or alpha', and two regulatory beta subunits. The closely related gene paralog encoding the alpha, or alpha 1 subunit (CSNK2A1, Gene ID: 1457) is found on chromosome 20. An intronic variant in this gene (alpha 2) may be associated with leukocyte telomere length in a South Asian population. A related transcribed pseudogene is found on chromosome 11. [provided by RefSeq, Aug 2017]

CSNK2A2 links:

ENSG00000260927 (HGNC:):

ENSG00000260927 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=-0.76).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2	NM_001896.4 link	c.*18-2669G>A	intron_variant	Intron 11 of 11	ENST00000262506.8	NP_001887.1	P19784
CSNK2A2	XM_047433626.1 link	c.*3049G>A	3_prime_UTR_variant	Exon 11 of 11		XP_047289582.1
CSNK2A2	XM_017022945.2 link	c.*18-2669G>A	intron_variant	Intron 7 of 7		XP_016878434.1
CSNK2A2	XM_005255801.4 link	c.*18-2669G>A	intron_variant	Intron 10 of 10		XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8 link	c.*18-2669G>A		intron_variant	Intron 11 of 11	1	NM_001896.4	ENSP00000262506.3		P19784

Frequencies

GnomAD3 genomes

AF:

0.373

AC:

56617

AN:

151868

Hom.:

11036

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.500

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.470

Gnomad EAS

AF:

0.199

Gnomad SAS

AF:

0.326

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.422

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.545

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.536

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.373

AC:

56629

AN:

151986

Hom.:

11031

Cov.:

AF XY:

0.368

AC XY:

27296

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.265

AC:

11000

AN:

41450

American (AMR)

AF:

0.344

AC:

5261

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.470

AC:

1631

AN:

3470

East Asian (EAS)

AF:

0.198

AC:

1021

AN:

5156

South Asian (SAS)

AF:

0.327

AC:

1574

AN:

4818

European-Finnish (FIN)

AF:

0.391

AC:

4119

AN:

10548

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.450

AC:

30566

AN:

67950

Other (OTH)

AF:

0.420

AC:

884

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1805

3610

5414

7219

9024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

548

1096

1644

2192

2740

<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:

0.423

Hom.:

53923

Bravo

AF:

0.362

Asia WGS

AF:

0.280

AC:

975

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

9.0

(source)

DANN

Benign

0.81

PhyloP100

0.13

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over