chr16-58161022-C-T
Variant names:
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
NM_001896.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.133
Publications
13 publications found
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]
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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 | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSNK2A2 | NM_001896.4 | c.*18-2669G>A | intron_variant | Intron 11 of 11 | ENST00000262506.8 | NP_001887.1 | ||
CSNK2A2 | XM_047433626.1 | c.*3049G>A | 3_prime_UTR_variant | Exon 11 of 11 | XP_047289582.1 | |||
CSNK2A2 | XM_017022945.2 | c.*18-2669G>A | intron_variant | Intron 7 of 7 | XP_016878434.1 | |||
CSNK2A2 | XM_005255801.4 | c.*18-2669G>A | intron_variant | Intron 10 of 10 | XP_005255858.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.373 AC: 56617AN: 151868Hom.: 11036 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
56617
AN:
151868
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.500 AC: 16AN: 32Hom.: 4 Cov.: 0 AF XY: 0.545 AC XY: 12AN XY: 22 show subpopulations
GnomAD4 exome
AF:
AC:
16
AN:
32
Hom.:
Cov.:
0
AF XY:
AC XY:
12
AN XY:
22
show subpopulations
African (AFR)
AF:
AC:
0
AN:
2
American (AMR)
AF:
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:
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: 56629AN: 151986Hom.: 11031 Cov.: 31 AF XY: 0.368 AC XY: 27296AN XY: 74264 show subpopulations
GnomAD4 genome
AF:
AC:
56629
AN:
151986
Hom.:
Cov.:
31
AF XY:
AC XY:
27296
AN XY:
74264
show subpopulations
African (AFR)
AF:
AC:
11000
AN:
41450
American (AMR)
AF:
AC:
5261
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
AC:
1631
AN:
3470
East Asian (EAS)
AF:
AC:
1021
AN:
5156
South Asian (SAS)
AF:
AC:
1574
AN:
4818
European-Finnish (FIN)
AF:
AC:
4119
AN:
10548
Middle Eastern (MID)
AF:
AC:
118
AN:
294
European-Non Finnish (NFE)
AF:
AC:
30566
AN:
67950
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
975
AN:
3476
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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