Variant chr6-31666793-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001320.7(CSNK2B):c.-11-28A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 1,582,494 control chromosomes in the GnomAD database, including 5,315 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 0.099 ( 894 hom., cov: 31)

Exomes 𝑓: 0.073 ( 4421 hom. )

Consequence

CSNK2B
NM_001320.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.02

Variant links:

Genes affected

CSNK2B (HGNC:2460): (casein kinase 2 beta) This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme is composed of three subunits, alpha, alpha prime and beta, which form a tetrameric holoenzyme. The alpha and alpha prime subunits are catalytic, while the beta subunit serves regulatory functions. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

CSNK2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 3 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 6-31666793-A-C is Benign according to our data. Variant chr6-31666793-A-C is described in ClinVar as [Benign]. Clinvar id is 1244893.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2B	NM_001320.7 linkuse as main transcript	c.-11-28A>C		intron_variant		ENST00000375882.7
CSNK2B	NM_001282385.2 linkuse as main transcript	c.-11-28A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2B	ENST00000375882.7 linkuse as main transcript	c.-11-28A>C		intron_variant		1	NM_001320.7	P1

Frequencies

GnomAD3 genomes

AF:

0.0992

AC:

15079

AN:

151984

Hom.:

896

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.0668

Gnomad ASJ

AF:

0.0750

Gnomad EAS

AF:

0.0782

Gnomad SAS

AF:

0.124

Gnomad FIN

AF:

0.0826

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0764

Gnomad OTH

AF:

0.0977

GnomAD3 exomes

AF:

0.0835

AC:

20290

AN:

243070

Hom.:

1008

AF XY:

0.0846

AC XY:

11107

AN XY:

131252

show subpopulations

Gnomad AFR exome

AF:

0.160

Gnomad AMR exome

AF:

0.0537

Gnomad ASJ exome

AF:

0.0768

Gnomad EAS exome

AF:

0.0959

Gnomad SAS exome

AF:

0.109

Gnomad FIN exome

AF:

0.0801

Gnomad NFE exome

AF:

0.0739

Gnomad OTH exome

AF:

0.0796

GnomAD4 exome

AF:

0.0729

AC:

104246

AN:

1430392

Hom.:

4421

Cov.:

AF XY:

0.0740

AC XY:

52617

AN XY:

710722

show subpopulations

Gnomad4 AFR exome

AF:

0.164

Gnomad4 AMR exome

AF:

0.0566

Gnomad4 ASJ exome

AF:

0.0787

Gnomad4 EAS exome

AF:

0.0461

Gnomad4 SAS exome

AF:

0.115

Gnomad4 FIN exome

AF:

0.0795

Gnomad4 NFE exome

AF:

0.0678

Gnomad4 OTH exome

AF:

0.0760

GnomAD4 genome

AF:

0.0991

AC:

15080

AN:

152102

Hom.:

894

Cov.:

AF XY:

0.0994

AC XY:

7390

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.0666

Gnomad4 ASJ

AF:

0.0750

Gnomad4 EAS

AF:

0.0787

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.0826

Gnomad4 NFE

AF:

0.0764

Gnomad4 OTH

AF:

0.0967

Alfa

AF:

0.0813

Hom.:

365

Bravo

AF:

0.101

Asia WGS

AF:

0.0880

AC:

306

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.66

BranchPoint Hunter

3.0

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

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