16-58161022-C-T

Position:

• chr16-58161022-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001896.4(CSNK2A2):​c.*18-2669G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 152,018 control chromosomes in the GnomAD database, including 11,035 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.37 (11031 hom., cov: 31)
  • Exomes 𝑓: 0.50 (4 hom.)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2A2	NM_001896.4	c.*18-2669G>A		intron_variant		ENST00000262506.8
CSNK2A2	XM_047433626.1	c.*3049G>A		3_prime_UTR_variant	11/11
CSNK2A2	XM_005255801.4	c.*18-2669G>A		intron_variant
CSNK2A2	XM_017022945.2	c.*18-2669G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.*18-2669G>A		intron_variant		1	NM_001896.4	P1
	ENST00000569580.2	n.2476C>T		non_coding_transcript_exon_variant	4/4	4

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56617 AN: 151868 Hom.: 11036 Cov.: 31

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.422

GnomAD4 exome AF: 0.500 AC: 16 AN: 32 Hom.: 4 Cov.: 0 AF XY: 0.545 AC XY: 12 AN XY: 22

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.536

GnomAD4 genome AF: 0.373 AC: 56629 AN: 151986 Hom.: 11031 Cov.: 31 AF XY: 0.368 AC XY: 27296 AN XY: 74264

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.420

Alfa AF: 0.436 Hom.: 25571

Bravo AF: 0.362

Asia WGS AF: 0.280 AC: 975 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.0
DANN	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs37358; hg19: chr16-58194926;