20-478765-CAAAAAAAA-CAAAAAAA

Variant names:

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

Variant summary

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

The ENST00000400227.8(CSNK2A1):​c.1061-6delT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0060 (1 hom., cov: 27)
  • Exomes 𝑓: 0.26 (0 hom.)
  • Failed GnomAD Quality Control
• 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: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00 AC: 676 AN: 113926 Hom.: 1 Cov.: 27 FAILED QC

Gnomad AFR AF: 0.00801

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00361

Gnomad ASJ AF: 0.000363

Gnomad EAS AF: 0.00122

Gnomad SAS AF: 0.00170

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0115

Gnomad NFE AF: 0.00336

Gnomad OTH AF: 0.00729

GnomAD3 exomes AF: 0.311 AC: 489 AN: 1572 Hom.: 0 AF XY: 0.319 AC XY: 306 AN XY: 958

Gnomad AFR exome AF: 0.375

Gnomad AMR exome AF: 0.305

Gnomad ASJ exome AF: 0.450

Gnomad EAS exome AF: 0.286

Gnomad SAS exome AF: 0.316

Gnomad FIN exome AF: 0.125

Gnomad NFE exome AF: 0.301

Gnomad OTH exome AF: 0.345

GnomAD4 exome AF: 0.260 AC: 15951 AN: 61318 Hom.: 0 Cov.: 0 AF XY: 0.260 AC XY: 9400 AN XY: 36096

Gnomad4 AFR exome AF: 0.217

Gnomad4 AMR exome AF: 0.240

Gnomad4 ASJ exome AF: 0.256

Gnomad4 EAS exome AF: 0.212

Gnomad4 SAS exome AF: 0.262

Gnomad4 FIN exome AF: 0.263

Gnomad4 NFE exome AF: 0.261

Gnomad4 OTH exome AF: 0.254

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00596 AC: 679 AN: 113904 Hom.: 1 Cov.: 27 AF XY: 0.00629 AC XY: 341 AN XY: 54240

Gnomad4 AFR AF: 0.00809

Gnomad4 AMR AF: 0.00361

Gnomad4 ASJ AF: 0.000363

Gnomad4 EAS AF: 0.00123

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.00336

Gnomad4 OTH AF: 0.00728

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;