rs6416862

chr17-82271464-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• 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/exons	MANE	UniProt
CSNK1D	NM_001893.6	c.76+1842G>A		intron_variant		ENST00000314028.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1D	ENST00000314028.11	c.76+1842G>A		intron_variant		1	NM_001893.6	A1

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

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.0499

Gnomad4 ASJ AF: 0.00605

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.0300

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00603

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0395 Hom.: 921

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

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: rs6416862; hg19: chr17-80229340;