chr16-58165848-G-T

Position:

• chr16-58165848-G-T

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.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

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 16-58165848-G-T is Benign according to our data. Variant chr16-58165848-G-T is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.828-140C>A		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.828-140C>A		intron_variant			XP_047289582.1
CSNK2A2	XM_017022945.2	c.504-140C>A		intron_variant			XP_016878434.1
CSNK2A2	XM_005255801.4	c.417-140C>A		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.828-140C>A		intron_variant		1	NM_001896.4	ENSP00000262506.3

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

Gnomad4 AFR exome AF: 0.636

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.447

Gnomad4 EAS exome AF: 0.815

Gnomad4 SAS exome AF: 0.637

Gnomad4 FIN exome AF: 0.582

Gnomad4 NFE exome AF: 0.512

Gnomad4 OTH exome AF: 0.546

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

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.794

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.527

Alfa AF: 0.414 Hom.: 1091

Bravo AF: 0.587

Asia WGS AF: 0.704 AC: 2444 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	clinical testing	GeneDx	Nov 11, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.54

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: rs2242443; hg19: chr16-58199752;