rs4789846

Variant names:

• chr17-82267669-T-C
• rs4789846
• NM_001893.6:c.77-1873A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001893.6(CSNK1D):​c.77-1873A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,286 control chromosomes in the GnomAD database, including 60,676 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 0.89 (60676 hom., cov: 33)
• Consequence: CSNK1D NM_001893.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.104
• Publications: 17 publications found

Genes affected

CSNK1D (HGNC:2452): (casein kinase 1 delta) This gene is a member of the casein kinase I (CKI) gene family whose members have been implicated in the control of cytoplasmic and nuclear processes, including DNA replication and repair. The encoded protein may also be involved in the regulation of apoptosis, circadian rhythm, microtubule dynamics, chromosome segregation, and p53-mediated effects on growth. The encoded protein is highly similar to the mouse and rat CK1 delta homologs. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2014]

CSNK1D Gene-Disease associations (from GenCC):

• advanced sleep phase syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001893.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	NM_001893.6	MANE Select	c.77-1873A>G		intron	N/A	NP_001884.2
	CSNK1D	NM_001363749.2		c.77-1873A>G		intron	N/A	NP_001350678.1	H7BYT1
	CSNK1D	NM_139062.4		c.77-1873A>G		intron	N/A	NP_620693.1	P48730-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1D	ENST00000314028.11	TSL:1 MANE Select	c.77-1873A>G		intron	N/A	ENSP00000324464.6	P48730-1
	CSNK1D	ENST00000392334.7	TSL:1	c.77-1873A>G		intron	N/A	ENSP00000376146.2	P48730-2
	CSNK1D	ENST00000865418.1		c.77-1873A>G		intron	N/A	ENSP00000535477.1

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135566 AN: 152168 Hom.: 60604 Cov.: 33

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.891 AC: 135698 AN: 152286 Hom.: 60676 Cov.: 33 AF XY: 0.891 AC XY: 66312 AN XY: 74460

African (AFR) AF: 0.965 AC: 40119 AN: 41574

American (AMR) AF: 0.897 AC: 13731 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2830 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3748 AN: 5180

South Asian (SAS) AF: 0.924 AC: 4459 AN: 4824

European-Finnish (FIN) AF: 0.879 AC: 9331 AN: 10610

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58556 AN: 68010

Other (OTH) AF: 0.864 AC: 1822 AN: 2110

Alfa AF: 0.870 Hom.: 110400

Bravo AF: 0.893

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.68
PhyloP100		0.10
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: rs4789846; hg19: chr17-80225545;