rs4789846

Positions:

• chr17-82267669-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNK1D	NM_001893.6	c.77-1873A>G		intron_variant		ENST00000314028.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1D	ENST00000314028.11	c.77-1873A>G		intron_variant		1	NM_001893.6	A1

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

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.816

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.879

Gnomad4 NFE AF: 0.861

Gnomad4 OTH AF: 0.864

Alfa AF: 0.867 Hom.: 80497

Bravo AF: 0.893

Asia WGS AF: 0.833 AC: 2898 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.1
DANN	Benign	0.68

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: rs4789846; hg19: chr17-80225545;