rs135763

Variant names:

• chr22-38312399-A-C
• rs135763
• NM_152221.3:c.76+1683T>G

Your query was ambiguous. Multiple possible variants found:

• chr22-38312399-A-C
• chr22-38312399-A-G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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:53829): (TPTEP2-CSNK1E readthrough) This locus represents naturally occurring readthrough transcription between the neighboring LOC400927 (transmembrane phosphoinositide 3-phosphatase and tensin homolog 2 pseudogene) and CSNK1E (casein kinase I isoform epsilon) genes on chromosome 22. The readthrough transcript encodes the same protein as the downstream gene product (casein kinase I isoform epsilon). [provided by RefSeq, Feb 2014]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CSNK1E	NM_152221.3	c.76+1683T>G		intron_variant	Intron 2 of 10	ENST00000396832.6	NP_689407.1
TPTEP2-CSNK1E	NM_001289912.2	c.76+1683T>G		intron_variant	Intron 6 of 14		NP_001276841.1
CSNK1E	NM_001894.5	c.76+1683T>G		intron_variant	Intron 2 of 10		NP_001885.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1E	ENST00000396832.6	c.76+1683T>G		intron_variant	Intron 2 of 10	1	NM_152221.3	ENSP00000380044.1
TPTEP2-CSNK1E	ENST00000400206.7	c.76+1683T>G		intron_variant	Intron 6 of 14	2		ENSP00000383067.2

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

African (AFR) AF: 0.868 AC: 36058 AN: 41540

American (AMR) AF: 0.750 AC: 11461 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2895 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4375 AN: 5172

South Asian (SAS) AF: 0.717 AC: 3461 AN: 4824

European-Finnish (FIN) AF: 0.813 AC: 8621 AN: 10604

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57125 AN: 68002

Other (OTH) AF: 0.826 AC: 1742 AN: 2108

Alfa AF: 0.828 Hom.: 44663

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
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs135763; hg19: chr22-38708404;