rs74019828

chr16-58175370-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001896.4(CSNK2A2):c.370-860C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.067 in 152,202 control chromosomes in the GnomAD database, including 415 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 0.067 (415 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2A2	NM_001896.4	c.370-860C>T		intron_variant		ENST00000262506.8
CSNK2A2	XM_005255801.4	c.-42-860C>T		intron_variant
CSNK2A2	XM_047433626.1	c.370-860C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.370-860C>T		intron_variant		1	NM_001896.4	P1

Frequencies

GnomAD3 genomes AF: 0.0669 AC: 10173 AN: 152084 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0533

Gnomad AMI AF: 0.00989

Gnomad AMR AF: 0.0478

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0601

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0670 AC: 10192 AN: 152202 Hom.: 415 Cov.: 32 AF XY: 0.0681 AC XY: 5065 AN XY: 74404

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0557

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0601

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.0667

Alfa AF: 0.0653 Hom.: 33

Bravo AF: 0.0627

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.4
Dann	Benign	0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs74019828; hg19: chr16-58209274;