16-58168027-T-C

Position:

• chr16-58168027-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001896.4(CSNK2A2):​c.514-232A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 152,284 control chromosomes in the GnomAD database, including 410 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.067 (410 hom., cov: 32)
• Consequence: CSNK2A2 NM_001896.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.559

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 16-58168027-T-C is Benign according to our data. Variant chr16-58168027-T-C is described in ClinVar as [Benign]. Clinvar id is 1287502.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK2A2	NM_001896.4	c.514-232A>G		intron_variant		ENST00000262506.8	NP_001887.1
CSNK2A2	XM_047433626.1	c.514-232A>G		intron_variant			XP_047289582.1
CSNK2A2	XM_017022945.2	c.190-232A>G		intron_variant			XP_016878434.1
CSNK2A2	XM_005255801.4	c.103-232A>G		intron_variant			XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8	c.514-232A>G		intron_variant		1	NM_001896.4	ENSP00000262506.3

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10125 AN: 152166 Hom.: 406 Cov.: 32

Gnomad AFR AF: 0.0532

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0477

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0569

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0608

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

GnomAD4 genome AF: 0.0666 AC: 10144 AN: 152284 Hom.: 410 Cov.: 32 AF XY: 0.0676 AC XY: 5030 AN XY: 74460

Gnomad4 AFR AF: 0.0533

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.0868

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0569

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0654

Alfa AF: 0.0651 Hom.: 32

Bravo AF: 0.0627

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.8
DANN	Benign	0.78

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: rs1875524; hg19: chr16-58201931;