rs6416862

Variant names:

• chr17-82271464-C-T
• rs6416862
• NM_001893.6:c.76+1842G>A

Variant summary

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

The NM_001893.6(CSNK1D):​c.76+1842G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,194 control chromosomes in the GnomAD database, including 3,880 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 0.13 (3880 hom., cov: 33)
• Consequence: CSNK1D NM_001893.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1D	NM_001893.6	c.76+1842G>A		intron_variant	Intron 1 of 8	ENST00000314028.11	NP_001884.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1D	ENST00000314028.11	c.76+1842G>A		intron_variant	Intron 1 of 8	1	NM_001893.6	ENSP00000324464.6

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19277 AN: 152076 Hom.: 3861 Cov.: 33

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0500

Gnomad ASJ AF: 0.00605

Gnomad EAS AF: 0.0113

Gnomad SAS AF: 0.0304

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.0848

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

GnomAD4 genome AF: 0.127 AC: 19344 AN: 152194 Hom.: 3880 Cov.: 33 AF XY: 0.123 AC XY: 9184 AN XY: 74440

African (AFR) AF: 0.426 AC: 17637 AN: 41450

American (AMR) AF: 0.0499 AC: 764 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00605 AC: 21 AN: 3470

East Asian (EAS) AF: 0.0112 AC: 58 AN: 5190

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4834

European-Finnish (FIN) AF: 0.000565 AC: 6 AN: 10618

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.00603 AC: 410 AN: 68020

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0561 Hom.: 1983

Bravo AF: 0.144

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.89
DANN	Benign	0.69
PhyloP100		-0.80
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: rs6416862; hg19: chr17-80229340;