20-483804-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_177559.3(CSNK2A1):c.*156del variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0792 in 149,322 control chromosomes in the GnomAD database, including 504 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.079 (504 hom., cov: 31)
  • Exomes 𝑓: 0.077 (664 hom.)
  • Failed GnomAD Quality Control
• Consequence: CSNK2A1 NM_177559.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.86

Genes affected

CSNK2A1 (HGNC:2457): (casein kinase 2 alpha 1) Casein kinase II 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 rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit. Multiple transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Apr 2018]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-483804-AT-A is Benign according to our data. Variant chr20-483804-AT-A is described in ClinVar as [Benign]. Clinvar id is 1273190.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK2A1	NM_177559.3	c.*156del		3_prime_UTR_variant	14/14	ENST00000217244.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK2A1	ENST00000217244.9	c.*156del		3_prime_UTR_variant	14/14	1	NM_177559.3	P1

Frequencies

GnomAD3 genomes AF: 0.0790 AC: 11789 AN: 149214 Hom.: 499 Cov.: 31

Gnomad AFR AF: 0.0955

Gnomad AMI AF: 0.0232

Gnomad AMR AF: 0.0660

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0694

Gnomad OTH AF: 0.0627

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0767 AC: 20640 AN: 268994 Hom.: 664 Cov.: 5 AF XY: 0.0777 AC XY: 10430 AN XY: 134226

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.101

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.0180

Gnomad4 SAS exome AF: 0.118

Gnomad4 FIN exome AF: 0.104

Gnomad4 NFE exome AF: 0.0733

Gnomad4 OTH exome AF: 0.0884

GnomAD4 genome AF: 0.0792 AC: 11824 AN: 149322 Hom.: 504 Cov.: 31 AF XY: 0.0793 AC XY: 5772 AN XY: 72782

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.0665

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0204

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0693

Gnomad4 OTH AF: 0.0620

Bravo AF: 0.0738

Asia WGS AF: 0.0870 AC: 305 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

Jul 03, 2018

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs111818075; hg19: chr20-464448;