chr16-58175370-G-A

Variant names:

• chr16-58175370-G-A
• rs74019828
• NM_001896.4:c.370-860C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 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 -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 rank	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.370-860C>T		intron_variant	Intron 4 of 11	ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.370-860C>T		intron_variant	Intron 4 of 10		XP_047289582.1
CSNK2A2	XM_005255801.4	c.-42-860C>T		intron_variant	Intron 3 of 10		XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.370-860C>T		intron_variant	Intron 4 of 11	1	NM_001896.4	ENSP00000262506.3

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

African (AFR) AF: 0.0534 AC: 2217 AN: 41542

American (AMR) AF: 0.0479 AC: 733 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0557 AC: 193 AN: 3468

East Asian (EAS) AF: 0.0868 AC: 449 AN: 5170

South Asian (SAS) AF: 0.202 AC: 974 AN: 4822

European-Finnish (FIN) AF: 0.0601 AC: 636 AN: 10580

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0709 AC: 4820 AN: 68012

Other (OTH) AF: 0.0667 AC: 141 AN: 2114

Alfa AF: 0.0689 Hom.: 614

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
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs74019828; hg19: chr16-58209274;