Variant 16-58166713-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1

The NM_001896.4(CSNK2A2):c.727-29T>G variant causes a intron change. The variant allele was found at a frequency of 0.0809 in 1,514,358 control chromosomes in the GnomAD database, including 6,137 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.070 ( 470 hom., cov: 32)

Exomes 𝑓: 0.082 ( 5667 hom. )

Consequence

CSNK2A2
NM_001896.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 6.07

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 3 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.19).

BP6

Variant 16-58166713-A-C is Benign according to our data. Variant chr16-58166713-A-C is described in ClinVar as [Benign]. Clinvar id is 1244609.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CSNK2A2	NM_001896.4 linkuse as main transcript	c.727-29T>G	intron_variant	ENST00000262506.8	NP_001887.1	P19784
CSNK2A2	XM_047433626.1 linkuse as main transcript	c.727-29T>G	intron_variant		XP_047289582.1
CSNK2A2	XM_017022945.2 linkuse as main transcript	c.403-29T>G	intron_variant		XP_016878434.1
CSNK2A2	XM_005255801.4 linkuse as main transcript	c.316-29T>G	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.727-29T>G		intron_variant		1	NM_001896.4	ENSP00000262506.3		P19784

Frequencies

GnomAD3 genomes

AF:

0.0699

AC:

10626

AN:

152044

Hom.:

464

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0548

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0483

Gnomad ASJ

AF:

0.0573

Gnomad EAS

AF:

0.163

Gnomad SAS

AF:

0.205

Gnomad FIN

AF:

0.0567

Gnomad MID

AF:

0.0701

Gnomad NFE

AF:

0.0709

Gnomad OTH

AF:

0.0627

GnomAD3 exomes

AF:

0.0874

AC:

21829

AN:

249684

Hom.:

1375

AF XY:

0.0934

AC XY:

12615

AN XY:

135124

show subpopulations

Gnomad AFR exome

AF:

0.0539

Gnomad AMR exome

AF:

0.0493

Gnomad ASJ exome

AF:

0.0599

Gnomad EAS exome

AF:

0.163

Gnomad SAS exome

AF:

0.208

Gnomad FIN exome

AF:

0.0531

Gnomad NFE exome

AF:

0.0684

Gnomad OTH exome

AF:

0.0722

GnomAD4 exome

AF:

0.0821

AC:

111818

AN:

1362196

Hom.:

5667

Cov.:

AF XY:

0.0863

AC XY:

59016

AN XY:

683900

show subpopulations

Gnomad4 AFR exome

AF:

0.0541

Gnomad4 AMR exome

AF:

0.0508

Gnomad4 ASJ exome

AF:

0.0628

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.201

Gnomad4 FIN exome

AF:

0.0514

Gnomad4 NFE exome

AF:

0.0739

Gnomad4 OTH exome

AF:

0.0790

GnomAD4 genome

AF:

0.0700

AC:

10646

AN:

152162

Hom.:

470

Cov.:

AF XY:

0.0714

AC XY:

5310

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.0549

Gnomad4 AMR

AF:

0.0484

Gnomad4 ASJ

AF:

0.0573

Gnomad4 EAS

AF:

0.163

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0567

Gnomad4 NFE

AF:

0.0709

Gnomad4 OTH

AF:

0.0692

Alfa

AF:

0.0669

Hom.:

Bravo

AF:

0.0667

Asia WGS

AF:

0.172

AC:

597

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 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.19

CADD

Benign

DANN

Benign

0.77

BranchPoint Hunter

3.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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