16-58167945-C-T

Variant names:

• chr16-58167945-C-T
• rs1875525
• NM_001896.4:c.514-150G>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.514-150G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 640,090 control chromosomes in the GnomAD database, including 2,520 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.067 (409 hom., cov: 32)
  • Exomes 𝑓: 0.081 (2111 hom.)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.689
• Publications: 5 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=-0.89).
• BP6: Variant 16-58167945-C-T is Benign according to our data. Variant chr16-58167945-C-T is described in ClinVar as Benign. ClinVar VariationId is 1224959.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.514-150G>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.514-150G>A		intron	N/A	ENSP00000262506.3	P19784
	CSNK2A2	ENST00000952604.1		c.553-150G>A		intron	N/A	ENSP00000622663.1
	CSNK2A2	ENST00000931140.1		c.514-150G>A		intron	N/A	ENSP00000601199.1

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10126 AN: 152080 Hom.: 405 Cov.: 32

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0708

Gnomad OTH AF: 0.0618

GnomAD4 exome AF: 0.0811 AC: 39565 AN: 487892 Hom.: 2111 AF XY: 0.0879 AC XY: 22866 AN XY: 260038

African (AFR) AF: 0.0527 AC: 692 AN: 13132

American (AMR) AF: 0.0500 AC: 1128 AN: 22566

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 903 AN: 15062

East Asian (EAS) AF: 0.104 AC: 3214 AN: 31040

South Asian (SAS) AF: 0.193 AC: 9382 AN: 48734

European-Finnish (FIN) AF: 0.0488 AC: 1638 AN: 33592

Middle Eastern (MID) AF: 0.0615 AC: 144 AN: 2340

European-Non Finnish (NFE) AF: 0.0701 AC: 20627 AN: 294192

Other (OTH) AF: 0.0675 AC: 1837 AN: 27234

GnomAD4 genome AF: 0.0667 AC: 10145 AN: 152198 Hom.: 409 Cov.: 32 AF XY: 0.0676 AC XY: 5029 AN XY: 74420

African (AFR) AF: 0.0533 AC: 2213 AN: 41524

American (AMR) AF: 0.0479 AC: 732 AN: 15290

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

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5188

South Asian (SAS) AF: 0.202 AC: 971 AN: 4814

European-Finnish (FIN) AF: 0.0569 AC: 603 AN: 10592

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

European-Non Finnish (NFE) AF: 0.0708 AC: 4814 AN: 68008

Other (OTH) AF: 0.0664 AC: 140 AN: 2108

Alfa AF: 0.0756 Hom.: 265

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	-0.89
CADD	Benign	1.3
DANN	Benign	0.59
PhyloP100		-0.69
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: rs1875525; hg19: chr16-58201849;