Variant 15-64171905-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2

The NM_022048.5(CSNK1G1):c.*26C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00846 in 1,588,852 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0087 ( 60 hom. )

Consequence

CSNK1G1
NM_022048.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.372

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 Likely_benign. Variant got -6 ACMG points.

BP6

Variant 15-64171905-G-A is Benign according to our data. Variant chr15-64171905-G-A is described in ClinVar as [Benign]. Clinvar id is 3770551.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 60 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G1	NM_022048.5 link	c.*26C>T	3_prime_UTR_variant	Exon 12 of 12	ENST00000303052.13	NP_071331.2	Q9HCP0-1A0A024R5W3
CSNK1G1	NM_001329606.2 link	c.*26C>T	3_prime_UTR_variant	Exon 12 of 12		NP_001316535.1	Q9HCP0-1A0A024R5W3
CSNK1G1	NM_001329605.2 link	c.1326-5825C>T	intron_variant	Intron 12 of 12		NP_001316534.1	U3KQB3
CSNK1G1	NM_001329607.2 link	c.1215-5825C>T	intron_variant	Intron 11 of 11		NP_001316536.1	Q8IXA3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1G1	ENST00000303052 link	c.*26C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_022048.5	ENSP00000305777.7		Q9HCP0-1

Frequencies

GnomAD3 genomes

AF:

0.00635

AC:

967

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00166

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0160

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00878

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.00593

AC:

1478

AN:

249366

Hom.:

AF XY:

0.00577

AC XY:

780

AN XY:

135290

show subpopulations

Gnomad AFR exome

AF:

0.00149

Gnomad AMR exome

AF:

0.00918

Gnomad ASJ exome

AF:

0.00268

Gnomad EAS exome

AF:

0.0000556

Gnomad SAS exome

AF:

0.000457

Gnomad FIN exome

AF:

0.00218

Gnomad NFE exome

AF:

0.00878

Gnomad OTH exome

AF:

0.00925

GnomAD4 exome

AF:

0.00869

AC:

12481

AN:

1436540

Hom.:

Cov.:

AF XY:

0.00829

AC XY:

5933

AN XY:

715904

show subpopulations

Gnomad4 AFR exome

AF:

0.00142

Gnomad4 AMR exome

AF:

0.00973

Gnomad4 ASJ exome

AF:

0.00254

Gnomad4 EAS exome

AF:

0.0000253

Gnomad4 SAS exome

AF:

0.000478

Gnomad4 FIN exome

AF:

0.00255

Gnomad4 NFE exome

AF:

0.0103

Gnomad4 OTH exome

AF:

0.00824

GnomAD4 genome

AF:

0.00635

AC:

967

AN:

152312

Hom.:

Cov.:

AF XY:

0.00587

AC XY:

437

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.00346

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00122

Gnomad4 NFE

AF:

0.00878

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.00645

Hom.:

Bravo

AF:

0.00722

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2025

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CSNK1G1: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

DANN

Benign

0.84

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.27

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.27

Position offset: 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