Variant chr15-64216564-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_022048.5(CSNK1G1):c.442C>T(p.Leu148=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.315 in 1,612,682 control chromosomes in the GnomAD database, including 100,590 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 20290 hom., cov: 31)

Exomes 𝑓: 0.30 ( 80300 hom. )

Consequence

CSNK1G1
NM_022048.5 splice_region, synonymous

Scores

Splicing: ADA: 0.001131

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.98

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 (BayesDel_noAF=-0.44).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CSNK1G1	NM_022048.5 linkuse as main transcript	c.442C>T	p.Leu148=	splice_region_variant, synonymous_variant	5/12	ENST00000303052.13
CSNK1G1	NM_001329605.2 linkuse as main transcript	c.442C>T	p.Leu148=	splice_region_variant, synonymous_variant	5/13
CSNK1G1	NM_001329607.2 linkuse as main transcript	c.442C>T	p.Leu148=	splice_region_variant, synonymous_variant	5/12
CSNK1G1	NM_001329606.2 linkuse as main transcript	c.442C>T	p.Leu148=	splice_region_variant, synonymous_variant	5/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNK1G1	ENST00000303052.13 linkuse as main transcript	c.442C>T	p.Leu148=	splice_region_variant, synonymous_variant	5/12	1	NM_022048.5		Q9HCP0-1

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66878

AN:

151898

Hom.:

20238

Cov.:

show subpopulations

Gnomad AFR

AF:

0.857

Gnomad AMI

AF:

0.348

Gnomad AMR

AF:

0.283

Gnomad ASJ

AF:

0.411

Gnomad EAS

AF:

0.133

Gnomad SAS

AF:

0.639

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.268

Gnomad OTH

AF:

0.407

GnomAD3 exomes

AF:

0.344

AC:

86006

AN:

249966

Hom.:

19865

AF XY:

0.355

AC XY:

47984

AN XY:

135236

show subpopulations

Gnomad AFR exome

AF:

0.871

Gnomad AMR exome

AF:

0.234

Gnomad ASJ exome

AF:

0.406

Gnomad EAS exome

AF:

0.125

Gnomad SAS exome

AF:

0.652

Gnomad FIN exome

AF:

0.229

Gnomad NFE exome

AF:

0.273

Gnomad OTH exome

AF:

0.315

GnomAD4 exome

AF:

0.302

AC:

441348

AN:

1460666

Hom.:

80300

Cov.:

AF XY:

0.312

AC XY:

226938

AN XY:

726680

show subpopulations

Gnomad4 AFR exome

AF:

0.886

Gnomad4 AMR exome

AF:

0.239

Gnomad4 ASJ exome

AF:

0.401

Gnomad4 EAS exome

AF:

0.145

Gnomad4 SAS exome

AF:

0.649

Gnomad4 FIN exome

AF:

0.234

Gnomad4 NFE exome

AF:

0.264

Gnomad4 OTH exome

AF:

0.338

GnomAD4 genome

AF:

0.441

AC:

66971

AN:

152016

Hom.:

20290

Cov.:

AF XY:

0.437

AC XY:

32509

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.857

Gnomad4 AMR

AF:

0.283

Gnomad4 ASJ

AF:

0.411

Gnomad4 EAS

AF:

0.133

Gnomad4 SAS

AF:

0.638

Gnomad4 FIN

AF:

0.231

Gnomad4 NFE

AF:

0.268

Gnomad4 OTH

AF:

0.402

Alfa

AF:

0.296

Hom.:

15416

Bravo

AF:

0.457

Asia WGS

AF:

0.398

AC:

1384

AN:

3478

EpiCase

AF:

0.287

EpiControl

AF:

0.290

ClinVar

Not reported in ClinVar

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

dbscSNV1_ADA

Benign

0.0011

dbscSNV1_RF

Benign

0.048

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over