Variant 16-58165766-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001896.4(CSNK2A2):c.828-58G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,554,906 control chromosomes in the GnomAD database, including 29,364 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.23 ( 4677 hom., cov: 33)

Exomes 𝑓: 0.18 ( 24687 hom. )

Consequence

CSNK2A2
NM_001896.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.60

Variant links:

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 links:

CSNK2A2 (HGNC:):

CSNK2A2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 16-58165766-C-T is Benign according to our data. Variant chr16-58165766-C-T is described in ClinVar as [Benign]. Clinvar id is 1280045.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CSNK2A2	NM_001896.4 linkuse as main transcript	c.828-58G>A	intron_variant	ENST00000262506.8	NP_001887.1	P19784
CSNK2A2	XM_047433626.1 linkuse as main transcript	c.828-58G>A	intron_variant		XP_047289582.1
CSNK2A2	XM_017022945.2 linkuse as main transcript	c.504-58G>A	intron_variant		XP_016878434.1
CSNK2A2	XM_005255801.4 linkuse as main transcript	c.417-58G>A	intron_variant		XP_005255858.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK2A2	ENST00000262506.8 linkuse as main transcript	c.828-58G>A		intron_variant		1	NM_001896.4	ENSP00000262506.3		P19784

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35450

AN:

152012

Hom.:

4667

Cov.:

show subpopulations

Gnomad AFR

AF:

0.334

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.165

Gnomad EAS

AF:

0.130

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.275

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.169

Gnomad OTH

AF:

0.208

GnomAD4 exome

AF:

0.181

AC:

253423

AN:

1402776

Hom.:

24687

AF XY:

0.177

AC XY:

123132

AN XY:

695598

show subpopulations

Gnomad4 AFR exome

AF:

0.348

Gnomad4 AMR exome

AF:

0.367

Gnomad4 ASJ exome

AF:

0.157

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.122

Gnomad4 FIN exome

AF:

0.269

Gnomad4 NFE exome

AF:

0.170

Gnomad4 OTH exome

AF:

0.184

GnomAD4 genome

AF:

0.233

AC:

35490

AN:

152130

Hom.:

4677

Cov.:

AF XY:

0.236

AC XY:

17570

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.334

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.165

Gnomad4 EAS

AF:

0.131

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.275

Gnomad4 NFE

AF:

0.169

Gnomad4 OTH

AF:

0.204

Alfa

AF:

0.201

Hom.:

532

Bravo

AF:

0.242

Asia WGS

AF:

0.152

AC:

530

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

DANN

Benign

0.80

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over