20-483804-ATTT-ATTTT

Variant names:

• chr20-483804-A-AT
• rs111818075
• NM_177559.3:c.*156dupA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_177559.3(CSNK2A1):​c.*156dupA variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00493 in 416,610 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00025 (1 hom., cov: 31)
  • Exomes 𝑓: 0.0075 (0 hom.)
• Consequence: CSNK2A1 NM_177559.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• 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 -8 ACMG points.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000254 (38/149364) while in subpopulation SAS AF= 0.00064 (3/4690). AF 95% confidence interval is 0.000271. There are 1 homozygotes in gnomad4. There are 16 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 38 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A1	NM_177559.3	c.*156dupA		3_prime_UTR_variant	Exon 14 of 14	ENST00000217244.9	NP_808227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A1	ENST00000217244	c.*156dupA		3_prime_UTR_variant	Exon 14 of 14	1	NM_177559.3	ENSP00000217244.3

Frequencies

GnomAD3 genomes AF: 0.000255 AC: 38 AN: 149256 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.000147

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.000639

Gnomad FIN AF: 0.000199

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000388

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00754 AC: 2016 AN: 267246 Hom.: 0 Cov.: 5 AF XY: 0.00761 AC XY: 1014 AN XY: 133232

Gnomad4 AFR exome AF: 0.00834

Gnomad4 AMR exome AF: 0.00575

Gnomad4 ASJ exome AF: 0.00531

Gnomad4 EAS exome AF: 0.00799

Gnomad4 SAS exome AF: 0.00674

Gnomad4 FIN exome AF: 0.00628

Gnomad4 NFE exome AF: 0.00779

Gnomad4 OTH exome AF: 0.00797

GnomAD4 genome AF: 0.000254 AC: 38 AN: 149364 Hom.: 1 Cov.: 31 AF XY: 0.000220 AC XY: 16 AN XY: 72802

Gnomad4 AFR AF: 0.000147

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.000640

Gnomad4 FIN AF: 0.000199

Gnomad4 NFE AF: 0.000388

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

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;