rs6001090

chr22-38300173-G-Achr22-38300173-G-Cchr22-38300173-G-T

Variant summary

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

The NM_152221.3(CSNK1E):c.566-108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0264 in 1,029,526 control chromosomes in the GnomAD database, including 3,502 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 0.097 (2210 hom., cov: 33)
  • Exomes 𝑓: 0.014 (1292 hom.)
• Consequence: CSNK1E NM_152221.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

Genes affected

CSNK1E (HGNC:2453): (casein kinase 1 epsilon) The protein encoded by this gene is a serine/threonine protein kinase and a member of the casein kinase I protein family, whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein is found in the cytoplasm as a monomer and can phosphorylate a variety of proteins, including itself. This protein has been shown to phosphorylate period, a circadian rhythm protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]

TPTEP2-CSNK1E (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1E	NM_152221.3	c.566-108C>T		intron_variant		ENST00000396832.6
TPTEP2-CSNK1E	NM_001289912.2	c.566-108C>T		intron_variant
CSNK1E	NM_001894.5	c.566-108C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1E	ENST00000396832.6	c.566-108C>T		intron_variant		1	NM_152221.3	P1

Frequencies

GnomAD3 genomes AF: 0.0963 AC: 14641 AN: 152108 Hom.: 2201 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0386

Gnomad ASJ AF: 0.00115

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.0342

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.00332

Gnomad OTH AF: 0.0660

GnomAD4 exome AF: 0.0143 AC: 12505 AN: 877300 Hom.: 1292 AF XY: 0.0142 AC XY: 6284 AN XY: 442072

Gnomad4 AFR exome AF: 0.330

Gnomad4 AMR exome AF: 0.0261

Gnomad4 ASJ exome AF: 0.00224

Gnomad4 EAS exome AF: 0.00847

Gnomad4 SAS exome AF: 0.0335

Gnomad4 FIN exome AF: 0.0000287

Gnomad4 NFE exome AF: 0.00234

Gnomad4 OTH exome AF: 0.0299

GnomAD4 genome AF: 0.0965 AC: 14692 AN: 152226 Hom.: 2210 Cov.: 33 AF XY: 0.0946 AC XY: 7039 AN XY: 74422

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.0385

Gnomad4 ASJ AF: 0.00115

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.0334

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00332

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0274 Hom.: 452

Bravo AF: 0.108

Asia WGS AF: 0.0570 AC: 197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.31
Dann	Benign	0.53

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: rs6001090; hg19: chr22-38696178; COSMIC: COSV63290606; COSMIC: COSV63290606;