Genetic Variant CSNK1G2:c.188-33C>T (chr19-1978272-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001319.7(CSNK1G2):c.188-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,611,286 control chromosomes in the GnomAD database, including 12,183 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 3385 hom., cov: 32)

Exomes 𝑓: 0.098 ( 8798 hom. )

Consequence

CSNK1G2
NM_001319.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233

Publications

8 publications found

Variant links:

Genes affected

CSNK1G2 (HGNC:2455): (casein kinase 1 gamma 2) Enables protein serine/threonine kinase activity. Involved in peptidyl-serine phosphorylation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CSNK1G2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001319.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G2	NM_001319.7	MANE Select	c.188-33C>T		intron	N/A	NP_001310.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CSNK1G2	ENST00000255641.13	TSL:1 MANE Select	c.188-33C>T	intron	N/A	ENSP00000255641.7
CSNK1G2	ENST00000589385.5	TSL:5	c.134-33C>T	intron	N/A	ENSP00000468637.1
CSNK1G2	ENST00000591752.5	TSL:5	c.188-33C>T	intron	N/A	ENSP00000467214.2

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25411

AN:

151870

Hom.:

3380

Cov.:

show subpopulations

Gnomad AFR

AF:

0.373

Gnomad AMI

AF:

0.0833

Gnomad AMR

AF:

0.0972

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.0936

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0648

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0866

Gnomad OTH

AF:

0.151

GnomAD2 exomes

AF:

0.108

AC:

27018

AN:

249838

AF XY:

0.104

show subpopulations

Gnomad AFR exome

AF:

0.379

Gnomad AMR exome

AF:

0.0762

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.0894

Gnomad FIN exome

AF:

0.0653

Gnomad NFE exome

AF:

0.0853

Gnomad OTH exome

AF:

0.0906

GnomAD4 exome

AF:

0.0978

AC:

142706

AN:

1459298

Hom.:

8798

Cov.:

AF XY:

0.0976

AC XY:

70884

AN XY:

725966

show subpopulations

African (AFR)

AF:

0.391

AC:

13053

AN:

33392

American (AMR)

AF:

0.0762

AC:

3404

AN:

44698

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

3752

AN:

26096

East Asian (EAS)

AF:

0.0807

AC:

3202

AN:

39692

South Asian (SAS)

AF:

0.119

AC:

10276

AN:

86208

European-Finnish (FIN)

AF:

0.0643

AC:

3401

AN:

52890

Middle Eastern (MID)

AF:

0.0817

AC:

435

AN:

5322

European-Non Finnish (NFE)

AF:

0.0888

AC:

98685

AN:

1110758

Other (OTH)

AF:

0.108

AC:

6498

AN:

60242

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

5963

11926

17890

23853

29816

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3910

7820

11730

15640

19550

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.167

AC:

25443

AN:

151988

Hom.:

3385

Cov.:

AF XY:

0.165

AC XY:

12287

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.372

AC:

15421

AN:

41406

American (AMR)

AF:

0.0970

AC:

1483

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.137

AC:

476

AN:

3470

East Asian (EAS)

AF:

0.0933

AC:

482

AN:

5168

South Asian (SAS)

AF:

0.124

AC:

598

AN:

4834

European-Finnish (FIN)

AF:

0.0648

AC:

687

AN:

10594

Middle Eastern (MID)

AF:

0.0748

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0866

AC:

5883

AN:

67920

Other (OTH)

AF:

0.150

AC:

315

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

936

1871

2807

3742

4678

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.110

Hom.:

4698

Bravo

AF:

0.177

Asia WGS

AF:

0.121

AC:

421

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.98

(source)

DANN

Benign

0.48

PhyloP100

-0.23

PromoterAI

-0.0019

Neutral

(source)

RBP_binding_hub_radar

0.67

RBP_regulation_power_radar

2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over