20-478765-CAAAAAAAA-CAAAAAAAAA

Variant names:

• chr20-478765-C-CA
• rs750062577
• NM_177559.3:c.*5195dupT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000400227.8(CSNK2A1):​c.1061-6dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0932 in 175,478 control chromosomes in the GnomAD database, including 840 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.10 (840 hom., cov: 27)
  • Exomes 𝑓: 0.072 (0 hom.)
• Consequence: CSNK2A1 ENST00000400227.8 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A1	NM_177559.3	c.*5195dupT		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.*5195dupT		3_prime_UTR_variant	Exon 14 of 14	1	NM_177559.3	ENSP00000217244.3

Frequencies

GnomAD3 genomes AF: 0.104 AC: 11891 AN: 113896 Hom.: 837 Cov.: 27

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0494

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0512

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0397

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.0530

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.107

GnomAD3 exomes AF: 0.0585 AC: 92 AN: 1572 Hom.: 0 AF XY: 0.0574 AC XY: 55 AN XY: 958

Gnomad AFR exome AF: 0.0313

Gnomad AMR exome AF: 0.0788

Gnomad ASJ exome AF: 0.0500

Gnomad EAS exome AF: 0.0408

Gnomad SAS exome AF: 0.0485

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0616

Gnomad OTH exome AF: 0.0345

GnomAD4 exome AF: 0.0723 AC: 4456 AN: 61602 Hom.: 0 Cov.: 0 AF XY: 0.0742 AC XY: 2690 AN XY: 36276

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.0938

Gnomad4 ASJ exome AF: 0.0641

Gnomad4 EAS exome AF: 0.0788

Gnomad4 SAS exome AF: 0.0774

Gnomad4 FIN exome AF: 0.0772

Gnomad4 NFE exome AF: 0.0677

Gnomad4 OTH exome AF: 0.0793

GnomAD4 genome AF: 0.105 AC: 11906 AN: 113876 Hom.: 840 Cov.: 27 AF XY: 0.105 AC XY: 5687 AN XY: 54224

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0512

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.0400

Gnomad4 FIN AF: 0.0651

Gnomad4 NFE AF: 0.0503

Gnomad4 OTH AF: 0.107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs750062577; hg19: chr20-459409;