rs9267531

chr6-31668965-A-G

Variant summary

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

The NM_001320.7(CSNK2B):c.292-132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 675,906 control chromosomes in the GnomAD database, including 2,999 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (536 hom., cov: 32)
  • Exomes 𝑓: 0.079 (2463 hom.)
• Consequence: CSNK2B NM_001320.7 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.23

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 6-31668965-A-G is Benign according to our data. Variant chr6-31668965-A-G is described in ClinVar as [Benign]. Clinvar id is 1182177.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2B	NM_001320.7	c.292-132A>G		intron_variant		ENST00000375882.7
CSNK2B	NM_001282385.2	c.292-132A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2B	ENST00000375882.7	c.292-132A>G		intron_variant		1	NM_001320.7	P1

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11122 AN: 152156 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.0398

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0560

GnomAD4 exome AF: 0.0791 AC: 41426 AN: 523632 Hom.: 2463 Cov.: 6 AF XY: 0.0755 AC XY: 20851 AN XY: 276028

Gnomad4 AFR exome AF: 0.0525

Gnomad4 AMR exome AF: 0.0264

Gnomad4 ASJ exome AF: 0.0421

Gnomad4 EAS exome AF: 0.0000620

Gnomad4 SAS exome AF: 0.00264

Gnomad4 FIN exome AF: 0.0813

Gnomad4 NFE exome AF: 0.107

Gnomad4 OTH exome AF: 0.0783

GnomAD4 genome AF: 0.0730 AC: 11122 AN: 152274 Hom.: 536 Cov.: 32 AF XY: 0.0681 AC XY: 5074 AN XY: 74458

Gnomad4 AFR AF: 0.0503

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0398

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00145

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.0554

Alfa AF: 0.101 Hom.: 661

Bravo AF: 0.0694

Asia WGS AF: 0.00837 AC: 30 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

May 11, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.031
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs9267531; hg19: chr6-31636742;