16-58167069-C-T

Variant names:

• chr16-58167069-C-T
• rs2292028
• NM_001896.4:c.726+138G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001896.4(CSNK2A2):​c.726+138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 574,318 control chromosomes in the GnomAD database, including 8,392 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (2026 hom., cov: 32)
  • Exomes 𝑓: 0.17 (6366 hom.)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.125
• Publications: 4 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]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 16-58167069-C-T is Benign according to our data. Variant chr16-58167069-C-T is described in ClinVar as Benign. ClinVar VariationId is 1264105.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001896.4. 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
	CSNK2A2	NM_001896.4	MANE Select	c.726+138G>A		intron	N/A	NP_001887.1	P19784

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK2A2	ENST00000262506.8	TSL:1 MANE Select	c.726+138G>A		intron	N/A	ENSP00000262506.3	P19784
	CSNK2A2	ENST00000952604.1		c.765+138G>A		intron	N/A	ENSP00000622663.1
	CSNK2A2	ENST00000931140.1		c.726+138G>A		intron	N/A	ENSP00000601199.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21608 AN: 152022 Hom.: 2021 Cov.: 32

Gnomad AFR AF: 0.0469

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.140

GnomAD4 exome AF: 0.167 AC: 70424 AN: 422178 Hom.: 6366 AF XY: 0.164 AC XY: 35797 AN XY: 218386

African (AFR) AF: 0.0456 AC: 511 AN: 11200

American (AMR) AF: 0.321 AC: 4419 AN: 13750

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 1556 AN: 12324

East Asian (EAS) AF: 0.170 AC: 4835 AN: 28392

South Asian (SAS) AF: 0.127 AC: 3432 AN: 26930

European-Finnish (FIN) AF: 0.261 AC: 8453 AN: 32336

Middle Eastern (MID) AF: 0.114 AC: 344 AN: 3022

European-Non Finnish (NFE) AF: 0.160 AC: 43117 AN: 270074

Other (OTH) AF: 0.156 AC: 3757 AN: 24150

GnomAD4 genome AF: 0.142 AC: 21627 AN: 152140 Hom.: 2026 Cov.: 32 AF XY: 0.149 AC XY: 11088 AN XY: 74358

African (AFR) AF: 0.0470 AC: 1951 AN: 41532

American (AMR) AF: 0.269 AC: 4114 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3470

East Asian (EAS) AF: 0.131 AC: 676 AN: 5178

South Asian (SAS) AF: 0.116 AC: 558 AN: 4824

European-Finnish (FIN) AF: 0.264 AC: 2786 AN: 10552

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10657 AN: 67986

Other (OTH) AF: 0.137 AC: 290 AN: 2110

Alfa AF: 0.169 Hom.: 415

Bravo AF: 0.139

Asia WGS AF: 0.129 AC: 450 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs2292028; hg19: chr16-58200973; COSMIC: COSV52641413;