Variant 15-64204455-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_022048.5(CSNK1G1):c.985G>A(p.Val329Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0082 in 1,585,338 control chromosomes in the GnomAD database, including 73 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0059 ( 5 hom., cov: 31)

Exomes 𝑓: 0.0084 ( 68 hom. )

Consequence

CSNK1G1
NM_022048.5 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.02

Variant links:

Genes affected

CSNK1G1 (HGNC:2454): (casein kinase 1 gamma 1) This gene encodes a member of the casein kinase I gene family. This family is comprised of serine/threonine kinases that phosphorylate acidic proteins such as caseins. The encoded kinase plays a role in cell cycle checkpoint arrest in response to stalled replication forks by phosphorylating Claspin. A mutation in this gene may be associated with non-syndromic early-onset epilepsy (NSEOE). [provided by RefSeq, Jul 2016]

CSNK1G1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007820845).

BP6

Variant 15-64204455-C-T is Benign according to our data. Variant chr15-64204455-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2645442.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CSNK1G1	NM_022048.5 linkuse as main transcript	c.985G>A	p.Val329Ile	missense_variant	9/12	ENST00000303052.13	NP_071331.2
CSNK1G1	NM_001329605.2 linkuse as main transcript	c.985G>A	p.Val329Ile	missense_variant	9/13		NP_001316534.1
CSNK1G1	NM_001329607.2 linkuse as main transcript	c.985G>A	p.Val329Ile	missense_variant	9/12		NP_001316536.1
CSNK1G1	NM_001329606.2 linkuse as main transcript	c.985G>A	p.Val329Ile	missense_variant	9/12		NP_001316535.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNK1G1	ENST00000303052.13 linkuse as main transcript	c.985G>A	p.Val329Ile	missense_variant	9/12	1	NM_022048.5	ENSP00000305777		Q9HCP0-1

Frequencies

GnomAD3 genomes

AF:

0.00588

AC:

884

AN:

150314

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00139

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.00595

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000634

Gnomad FIN

AF:

0.00220

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00946

Gnomad OTH

AF:

0.00969

GnomAD3 exomes

AF:

0.00602

AC:

1389

AN:

230696

Hom.:

AF XY:

0.00589

AC XY:

735

AN XY:

124860

show subpopulations

Gnomad AFR exome

AF:

0.00128

Gnomad AMR exome

AF:

0.00470

Gnomad ASJ exome

AF:

0.00656

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00185

Gnomad FIN exome

AF:

0.00185

Gnomad NFE exome

AF:

0.00964

Gnomad OTH exome

AF:

0.00926

GnomAD4 exome

AF:

0.00845

AC:

12119

AN:

1434956

Hom.:

Cov.:

AF XY:

0.00819

AC XY:

5842

AN XY:

713228

show subpopulations

Gnomad4 AFR exome

AF:

0.00116

Gnomad4 AMR exome

AF:

0.00483

Gnomad4 ASJ exome

AF:

0.00636

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00201

Gnomad4 FIN exome

AF:

0.00208

Gnomad4 NFE exome

AF:

0.00993

Gnomad4 OTH exome

AF:

0.00840

GnomAD4 genome

AF:

0.00587

AC:

883

AN:

150382

Hom.:

Cov.:

AF XY:

0.00563

AC XY:

412

AN XY:

73232

show subpopulations

Gnomad4 AFR

AF:

0.00139

Gnomad4 AMR

AF:

0.00595

Gnomad4 ASJ

AF:

0.00404

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000636

Gnomad4 FIN

AF:

0.00220

Gnomad4 NFE

AF:

0.00944

Gnomad4 OTH

AF:

0.00962

Alfa

AF:

0.00881

Hom.:

Bravo

AF:

0.00635

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0103

AC:

ExAC

AF:

0.00604

AC:

733

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2023

CSNK1G1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.084

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Benign

0.91

DEOGEN2

Benign

0.036

T;T;T;.;T;T;T;T;T;.;T

Eigen

Benign

-0.11

Eigen_PC

Benign

0.15

FATHMM_MKL

Uncertain

0.96

LIST_S2

Benign

0.79

T;T;T;T;.;T;T;T;T;T;T

MetaRNN

Benign

0.0078

T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.62

N;.;.;.;.;.;.;.;.;.;.

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.63

PROVEAN

Benign

-0.60

N;.;.;.;.;.;.;.;.;.;.

REVEL

Benign

0.082

Sift

Benign

0.41

T;.;.;.;.;.;.;.;.;.;.

Sift4G

Benign

0.40

T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.0

B;.;B;.;.;.;.;.;.;.;.

Vest4

0.32

MVP

0.35

MPC

0.38

ClinPred

0.011

GERP RS

5.5

Varity_R

0.086

gMVP

0.36

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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