chr16-58164235-G-C

Position:

• chr16-58164235-G-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.977-88C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0659 in 1,212,984 control chromosomes in the GnomAD database, including 3,545 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.066 (430 hom., cov: 32)
  • Exomes 𝑓: 0.066 (3115 hom.)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.593

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=-0.87).
• BP6: Variant 16-58164235-G-C is Benign according to our data. Variant chr16-58164235-G-C is described in ClinVar as [Benign]. Clinvar id is 1274882.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.977-88C>G		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.977-88C>G		intron_variant			XP_047289582.1
CSNK2A2	XM_017022945.2	c.653-88C>G		intron_variant			XP_016878434.1
CSNK2A2	XM_005255801.4	c.566-88C>G		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.977-88C>G		intron_variant		1	NM_001896.4	ENSP00000262506.3

Frequencies

GnomAD3 genomes AF: 0.0659 AC: 10025 AN: 152108 Hom.: 427 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.0636

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0568

Gnomad OTH AF: 0.0531

GnomAD4 exome AF: 0.0659 AC: 69880 AN: 1060756 Hom.: 3115 AF XY: 0.0704 AC XY: 37852 AN XY: 537936

Gnomad4 AFR exome AF: 0.0850

Gnomad4 AMR exome AF: 0.0481

Gnomad4 ASJ exome AF: 0.0491

Gnomad4 EAS exome AF: 0.0705

Gnomad4 SAS exome AF: 0.184

Gnomad4 FIN exome AF: 0.0371

Gnomad4 NFE exome AF: 0.0572

Gnomad4 OTH exome AF: 0.0623

GnomAD4 genome AF: 0.0660 AC: 10048 AN: 152228 Hom.: 430 Cov.: 32 AF XY: 0.0666 AC XY: 4955 AN XY: 74434

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0449

Gnomad4 EAS AF: 0.0633

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.0350

Gnomad4 NFE AF: 0.0568

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0594 Hom.: 27

Bravo AF: 0.0654

Asia WGS AF: 0.112 AC: 388 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	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
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: rs2279803; hg19: chr16-58198139;