rs805257

chr6-31666416-A-Gchr6-31666416-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001320.7(CSNK2B):c.-12+208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 186,002 control chromosomes in the GnomAD database, including 18,415 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.45 (16150 hom., cov: 31)
  • Exomes 𝑓: 0.35 (2265 hom.)
• Consequence: CSNK2B NM_001320.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.834

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2B	NM_001320.7	c.-12+208A>G		intron_variant		ENST00000375882.7
CSNK2B	NM_001282385.2	c.-12+208A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2B	ENST00000375882.7	c.-12+208A>G		intron_variant		1	NM_001320.7	P1

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68540 AN: 151866 Hom.: 16128 Cov.: 31

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.443

GnomAD4 exome AF: 0.345 AC: 11738 AN: 34018 Hom.: 2265 Cov.: 4 AF XY: 0.347 AC XY: 6300 AN XY: 18144

Gnomad4 AFR exome AF: 0.597

Gnomad4 AMR exome AF: 0.380

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.379

Gnomad4 SAS exome AF: 0.331

Gnomad4 FIN exome AF: 0.434

Gnomad4 NFE exome AF: 0.330

Gnomad4 OTH exome AF: 0.338

GnomAD4 genome AF: 0.451 AC: 68607 AN: 151984 Hom.: 16150 Cov.: 31 AF XY: 0.454 AC XY: 33736 AN XY: 74298

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.446

Alfa AF: 0.393 Hom.: 16220

Bravo AF: 0.454

Asia WGS AF: 0.477 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.9
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs805257; hg19: chr6-31634193;