22-38294692-A-G

Position:

• chr22-38294692-A-G

Variant summary

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

The NM_152221.3(CSNK1E):​c.886-158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 152,014 control chromosomes in the GnomAD database, including 33,607 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 0.64 (33607 hom., cov: 31)
• Consequence: CSNK1E NM_152221.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1E	NM_152221.3	c.886-158T>C		intron_variant		ENST00000396832.6
TPTEP2-CSNK1E	NM_001289912.2	c.886-158T>C		intron_variant
CSNK1E	NM_001894.5	c.886-158T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1E	ENST00000396832.6	c.886-158T>C		intron_variant		1	NM_152221.3	P1

Frequencies

GnomAD3 genomes AF: 0.642 AC: 97559 AN: 151896 Hom.: 33594 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.642 AC: 97604 AN: 152014 Hom.: 33607 Cov.: 31 AF XY: 0.643 AC XY: 47762 AN XY: 74320

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.664

Alfa AF: 0.700 Hom.: 7426

Bravo AF: 0.627

Asia WGS AF: 0.682 AC: 2369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.13
DANN	Benign	0.57
RBP_binding_hub_radar		0.67
RBP_regulation_power_radar		1.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2075983; hg19: chr22-38690698;