rs6494466

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

2
Splicing: ADA: 0.001131
2

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]

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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 UniProt
CSNK1G1NM_022048.5 linkuse as main transcriptc.442C>T p.Leu148= splice_region_variant, synonymous_variant 5/12 ENST00000303052.13
CSNK1G1NM_001329605.2 linkuse as main transcriptc.442C>T p.Leu148= splice_region_variant, synonymous_variant 5/13
CSNK1G1NM_001329607.2 linkuse as main transcriptc.442C>T p.Leu148= splice_region_variant, synonymous_variant 5/12
CSNK1G1NM_001329606.2 linkuse as main transcriptc.442C>T p.Leu148= splice_region_variant, synonymous_variant 5/12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CSNK1G1ENST00000303052.13 linkuse as main transcriptc.442C>T p.Leu148= splice_region_variant, synonymous_variant 5/121 NM_022048.5 Q9HCP0-1

Frequencies

GnomAD3 genomes
AF:
0.440
AC:
66878
AN:
151898
Hom.:
20238
Cov.:
31
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.:
33
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.:
31
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
12
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.

Other links and lift over

dbSNP: rs6494466; hg19: chr15-64508763; COSMIC: COSV57311782; COSMIC: COSV57311782; API