22-38312399-A-C

Position:

• chr22-38312399-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.76+1683T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,208 control chromosomes in the GnomAD database, including 52,892 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 0.83 (52892 hom., cov: 33)
• Consequence: CSNK1E NM_152221.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.180

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1E	NM_152221.3	c.76+1683T>G		intron_variant		ENST00000396832.6
TPTEP2-CSNK1E	NM_001289912.2	c.76+1683T>G		intron_variant
CSNK1E	NM_001894.5	c.76+1683T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1E	ENST00000396832.6	c.76+1683T>G		intron_variant		1	NM_152221.3	P1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126628 AN: 152090 Hom.: 52840 Cov.: 33

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.824

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

GnomAD4 genome AF: 0.833 AC: 126743 AN: 152208 Hom.: 52892 Cov.: 33 AF XY: 0.827 AC XY: 61526 AN XY: 74420

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.813

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.826

Alfa AF: 0.821 Hom.: 21168

Bravo AF: 0.833

Asia WGS AF: 0.773 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.3
DANN	Benign	0.47

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: rs135763; hg19: chr22-38708404;