16-58184072-T-C

Position:

• chr16-58184072-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001896.4(CSNK2A2):​c.369+188A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,132 control chromosomes in the GnomAD database, including 1,953 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.14 (1953 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.283

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]

CSNK2A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 16-58184072-T-C is Benign according to our data. Variant chr16-58184072-T-C is described in ClinVar as [Benign]. Clinvar id is 1258164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.369+188A>G		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.369+188A>G		intron_variant			XP_047289582.1
CSNK2A2	XM_005255801.4	c.-43+188A>G		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.369+188A>G		intron_variant		1	NM_001896.4	ENSP00000262506.3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21475 AN: 152014 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.141 AC: 21469 AN: 152132 Hom.: 1953 Cov.: 32 AF XY: 0.144 AC XY: 10685 AN XY: 74356

Gnomad4 AFR AF: 0.0374

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.148

Alfa AF: 0.152 Hom.: 1104

Bravo AF: 0.141

Asia WGS AF: 0.265 AC: 918 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.4
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs3743579; hg19: chr16-58217976; COSMIC: COSV52641788;