rs2242443

Variant names:

• chr16-58165848-G-T
• rs2242443
• NM_001896.4:c.828-140C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-58165848-G-T
• chr16-58165848-G-A
• chr16-58165848-G-C

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.828-140C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 814,026 control chromosomes in the GnomAD database, including 127,204 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.58 (26029 hom., cov: 33)
  • Exomes 𝑓: 0.54 (101175 hom.)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.732
• 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=-0.87).
• BP6: Variant 16-58165848-G-T is Benign according to our data. Variant chr16-58165848-G-T is described in ClinVar as Benign. ClinVar VariationId is 1181877.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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.828-140C>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.828-140C>A		intron	N/A	ENSP00000262506.3	P19784
	CSNK2A2	ENST00000952604.1		c.867-140C>A		intron	N/A	ENSP00000622663.1
	CSNK2A2	ENST00000931140.1		c.828-140C>A		intron	N/A	ENSP00000601199.1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88403 AN: 151958 Hom.: 25995 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.525

GnomAD4 exome AF: 0.544 AC: 360425 AN: 661950 Hom.: 101175 AF XY: 0.548 AC XY: 184758 AN XY: 337288

African (AFR) AF: 0.636 AC: 9934 AN: 15630

American (AMR) AF: 0.667 AC: 10113 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 6454 AN: 14442

East Asian (EAS) AF: 0.815 AC: 24805 AN: 30442

South Asian (SAS) AF: 0.637 AC: 26835 AN: 42116

European-Finnish (FIN) AF: 0.582 AC: 20528 AN: 35248

Middle Eastern (MID) AF: 0.514 AC: 1668 AN: 3244

European-Non Finnish (NFE) AF: 0.512 AC: 242501 AN: 473460

Other (OTH) AF: 0.546 AC: 17587 AN: 32198

GnomAD4 genome AF: 0.582 AC: 88494 AN: 152076 Hom.: 26029 Cov.: 33 AF XY: 0.588 AC XY: 43711 AN XY: 74346

African (AFR) AF: 0.638 AC: 26466 AN: 41472

American (AMR) AF: 0.623 AC: 9516 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1617 AN: 3470

East Asian (EAS) AF: 0.794 AC: 4117 AN: 5182

South Asian (SAS) AF: 0.659 AC: 3177 AN: 4824

European-Finnish (FIN) AF: 0.597 AC: 6314 AN: 10570

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35605 AN: 67964

Other (OTH) AF: 0.527 AC: 1114 AN: 2112

Alfa AF: 0.431 Hom.: 1246

Bravo AF: 0.587

Asia WGS AF: 0.704 AC: 2444 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	-0.87
CADD	Benign	0.93
DANN	Benign	0.54
PhyloP100		-0.73
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: rs2242443; hg19: chr16-58199752;