chr16-58168027-T-C

Variant names:

• chr16-58168027-T-C
• rs1875524
• NM_001896.4:c.514-232A>G

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.514-232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,284 control chromosomes in the GnomAD database, including 410 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.067 (410 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.559
• Publications: 1 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=-0.84).
• BP6: Variant 16-58168027-T-C is Benign according to our data. Variant chr16-58168027-T-C is described in ClinVar as Benign. ClinVar VariationId is 1287502.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 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.514-232A>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.514-232A>G		intron	N/A	ENSP00000262506.3	P19784
	CSNK2A2	ENST00000952604.1		c.553-232A>G		intron	N/A	ENSP00000622663.1
	CSNK2A2	ENST00000931140.1		c.514-232A>G		intron	N/A	ENSP00000601199.1

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10125 AN: 152166 Hom.: 406 Cov.: 32

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0666 AC: 10144 AN: 152284 Hom.: 410 Cov.: 32 AF XY: 0.0676 AC XY: 5030 AN XY: 74460

African (AFR) AF: 0.0533 AC: 2214 AN: 41552

American (AMR) AF: 0.0479 AC: 733 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.0868 AC: 451 AN: 5194

South Asian (SAS) AF: 0.201 AC: 971 AN: 4828

European-Finnish (FIN) AF: 0.0569 AC: 603 AN: 10594

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

European-Non Finnish (NFE) AF: 0.0707 AC: 4811 AN: 68020

Other (OTH) AF: 0.0654 AC: 138 AN: 2110

Alfa AF: 0.0644 Hom.: 33

Bravo AF: 0.0627

Asia WGS AF: 0.120 AC: 417 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	-0.84
CADD	Benign	6.8
DANN	Benign	0.78
PhyloP100		-0.56
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: rs1875524; hg19: chr16-58201931;