NM_001896.4:c.369+188A>G

Variant names:

• chr16-58184072-T-C
• rs3743579
• NM_001896.4:c.369+188A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001896.4(CSNK2A2):​c.369+188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,132 control chromosomes in the GnomAD database, including 1,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.14 (1953 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.283
• 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 16-58184072-T-C is Benign according to our data. Variant chr16-58184072-T-C is described in ClinVar as Benign. ClinVar VariationId is 1258164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 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.369+188A>G		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.369+188A>G		intron	N/A	ENSP00000262506.3	P19784
	CSNK2A2	ENST00000952604.1		c.369+188A>G		intron	N/A	ENSP00000622663.1
	CSNK2A2	ENST00000931140.1		c.369+188A>G		intron	N/A	ENSP00000601199.1

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21475 AN: 152014 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.147

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.141 AC: 21469 AN: 152132 Hom.: 1953 Cov.: 32 AF XY: 0.144 AC XY: 10685 AN XY: 74356

African (AFR) AF: 0.0374 AC: 1554 AN: 41530

American (AMR) AF: 0.168 AC: 2566 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1841 AN: 5162

South Asian (SAS) AF: 0.262 AC: 1265 AN: 4820

European-Finnish (FIN) AF: 0.140 AC: 1478 AN: 10582

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11558 AN: 67990

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.159 Hom.: 1972

Bravo AF: 0.141

Asia WGS AF: 0.265 AC: 918 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.66
PhyloP100		-0.28
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

Other links and lift over

dbSNP: rs3743579; hg19: chr16-58217976; COSMIC: COSV52641788;