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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G2	NM_001319.7 link	c.188-33C>T		intron_variant	Intron 2 of 11	ENST00000255641.13	NP_001310.3	P78368

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK1G2	ENST00000255641.13 link	c.188-33C>T		intron_variant	Intron 2 of 11	1	NM_001319.7	ENSP00000255641.7		P78368

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over