Variant 17-82251406-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001893.6(CSNK1D):c.858C>T(p.Tyr286Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 1,614,106 control chromosomes in the GnomAD database, including 173 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0094 ( 8 hom., cov: 32)

Exomes 𝑓: 0.013 ( 165 hom. )

Consequence

CSNK1D
NM_001893.6 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.218

Variant links:

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 links:

SLC16A3 (HGNC:10924): (solute carrier family 16 member 3) Lactic acid and pyruvate transport across plasma membranes is catalyzed by members of the proton-linked monocarboxylate transporter (MCT) family, which has been designated solute carrier family-16. Each MCT appears to have slightly different substrate and inhibitor specificities and transport kinetics, which are related to the metabolic requirements of the tissues in which it is found. The MCTs, which include MCT1 (SLC16A1; MIM 600682) and MCT2 (SLC16A7; MIM 603654), are characterized by 12 predicted transmembrane domains (Price et al., 1998 [PubMed 9425115]).[supplied by OMIM, Mar 2008]

SLC16A3 links:

CSNK1D (HGNC:):

CSNK1D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP6

Variant 17-82251406-G-A is Benign according to our data. Variant chr17-82251406-G-A is described in ClinVar as [Benign]. Clinvar id is 3387900.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.218 with no splicing effect.

BS2

High AC in GnomAd4 at 1429 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK1D	NM_001893.6 linkuse as main transcript	c.858C>T	p.Tyr286Tyr	synonymous_variant	6/9	ENST00000314028.11	NP_001884.2	P48730-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK1D	ENST00000314028.11 linkuse as main transcript	c.858C>T	p.Tyr286Tyr	synonymous_variant	6/9	1	NM_001893.6	ENSP00000324464.6		P48730-1

Frequencies

GnomAD3 genomes

AF:

0.00939

AC:

1429

AN:

152160

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00203

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.00563

Gnomad ASJ

AF:

0.00749

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0128

Gnomad FIN

AF:

0.00782

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0155

Gnomad OTH

AF:

0.00863

GnomAD3 exomes

AF:

0.00994

AC:

2497

AN:

251312

Hom.:

AF XY:

0.0106

AC XY:

1443

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.00240

Gnomad AMR exome

AF:

0.00289

Gnomad ASJ exome

AF:

0.00854

Gnomad EAS exome

AF:

0.000218

Gnomad SAS exome

AF:

0.0112

Gnomad FIN exome

AF:

0.00790

Gnomad NFE exome

AF:

0.0148

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.0127

AC:

18506

AN:

1461828

Hom.:

165

Cov.:

AF XY:

0.0129

AC XY:

9358

AN XY:

727202

show subpopulations

Gnomad4 AFR exome

AF:

0.00245

Gnomad4 AMR exome

AF:

0.00322

Gnomad4 ASJ exome

AF:

0.00869

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.0123

Gnomad4 FIN exome

AF:

0.00929

Gnomad4 NFE exome

AF:

0.0141

Gnomad4 OTH exome

AF:

0.0116

GnomAD4 genome

AF:

0.00938

AC:

1429

AN:

152278

Hom.:

Cov.:

AF XY:

0.00921

AC XY:

686

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00200

Gnomad4 AMR

AF:

0.00562

Gnomad4 ASJ

AF:

0.00749

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0131

Gnomad4 FIN

AF:

0.00782

Gnomad4 NFE

AF:

0.0155

Gnomad4 OTH

AF:

0.00854

Alfa

AF:

0.0130

Hom.:

Bravo

AF:

0.00857

Asia WGS

AF:

0.00375

AC:

AN:

3478

EpiCase

AF:

0.0136

EpiControl

AF:

0.0147

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2024

CSNK1D: BP4, BP7, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.0

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over