chr16-58161022-C-T

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

2

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]

Genome browser will be placed here

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 HGVSp Effect Exon rank MANE Protein UniProt
CSNK2A2NM_001896.4 linkc.*18-2669G>A intron_variant Intron 11 of 11 ENST00000262506.8 NP_001887.1 P19784
CSNK2A2XM_047433626.1 linkc.*3049G>A 3_prime_UTR_variant Exon 11 of 11 XP_047289582.1
CSNK2A2XM_017022945.2 linkc.*18-2669G>A intron_variant Intron 7 of 7 XP_016878434.1
CSNK2A2XM_005255801.4 linkc.*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
CSNK2A2ENST00000262506.8 linkc.*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.:
31
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:
16
AN:
32
Hom.:
4
Cov.:
0
AF XY:
0.545
AC XY:
12
AN XY:
22
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
2
American (AMR)
AF:
0.500
AC:
1
AN:
2
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.536
AC:
15
AN:
28
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.531
Heterozygous variant carriers
0
1
1
2
2
3
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.:
31
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
0
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
0
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
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)

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

Other links and lift over

dbSNP: rs37358; hg19: chr16-58194926; API