rs1005473

chr22-38298367-A-C

Variant summary

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

The NM_152221.3(CSNK1E):c.885+419T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 151,900 control chromosomes in the GnomAD database, including 548 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 0.072 (548 hom., cov: 32)
• Consequence: CSNK1E NM_152221.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.18

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=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1E	NM_152221.3	c.885+419T>G		intron_variant		ENST00000396832.6
TPTEP2-CSNK1E	NM_001289912.2	c.885+419T>G		intron_variant
CSNK1E	NM_001894.5	c.885+419T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1E	ENST00000396832.6	c.885+419T>G		intron_variant		1	NM_152221.3	P1

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10969 AN: 151782 Hom.: 549 Cov.: 32

Gnomad AFR AF: 0.0540

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0616

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0722 AC: 10972 AN: 151900 Hom.: 548 Cov.: 32 AF XY: 0.0790 AC XY: 5871 AN XY: 74284

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0740

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0525

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0604 Hom.: 55

Bravo AF: 0.0765

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.6
Dann	Benign	0.72

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: rs1005473; hg19: chr22-38694373; COSMIC: COSV63290727; COSMIC: COSV63290727;