dbSNP rs2074882: CSNK1G2:c.-265-30G>A (chr19-1969478-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_001319.7(CSNK1G2):c.-265-30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00132 in 241,200 control chromosomes in the GnomAD database, including 4 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 0.00091 ( 1 hom., cov: 29)

Exomes 𝑓: 0.0020 ( 3 hom. )

Consequence

CSNK1G2
NM_001319.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.189

Publications

2 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=-0.83).

BS1

Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.000909 (138/151762) while in subpopulation EAS AF = 0.0223 (114/5114). AF 95% confidence interval is 0.019. There are 1 homozygotes in GnomAd4. There are 74 alleles in the male GnomAd4 subpopulation. Median coverage is 29. This position passed quality control check.

BS2

High AC in GnomAd4 at 138 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G2	NM_001319.7 link	c.-265-30G>A		intron_variant	Intron 1 of 11	ENST00000255641.13	NP_001310.3	P78368

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
CSNK1G2	ENST00000255641.13 link	c.-265-30G>A	intron_variant	Intron 1 of 11	1	NM_001319.7	ENSP00000255641.7	P78368
CSNK1G2	ENST00000589350.2 link	c.-265-30G>A	intron_variant	Intron 3 of 4	5		ENSP00000465106.1	K7EJC0
CSNK1G2	ENST00000591752.5 link	c.-265-30G>A	intron_variant	Intron 1 of 2	5		ENSP00000467214.2	K7EP38
CSNK1G2	ENST00000614707.1 link	n.96-30G>A	intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.000910

AC:

138

AN:

151644

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000485

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0222

Gnomad SAS

AF:

0.00188

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000133

Gnomad OTH

AF:

0.000960

GnomAD4 exome

AF:

0.00201

AC:

180

AN:

89438

Hom.:

Cov.:

AF XY:

0.00170

AC XY:

AN XY:

44832

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

3164

American (AMR)

AF:

0.00

AC:

AN:

2482

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3872

East Asian (EAS)

AF:

0.0214

AC:

171

AN:

7982

South Asian (SAS)

AF:

0.00

AC:

AN:

802

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5508

Middle Eastern (MID)

AF:

0.00

AC:

AN:

538

European-Non Finnish (NFE)

AF:

0.0000849

AC:

AN:

58874

Other (OTH)

AF:

0.000644

AC:

AN:

6216

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.000909

AC:

138

AN:

151762

Hom.:

Cov.:

AF XY:

0.000998

AC XY:

AN XY:

74134

show subpopulations

African (AFR)

AF:

0.0000483

AC:

AN:

41368

American (AMR)

AF:

0.000131

AC:

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3466

East Asian (EAS)

AF:

0.0223

AC:

114

AN:

5114

South Asian (SAS)

AF:

0.00188

AC:

AN:

4794

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10542

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000133

AC:

AN:

67912

Other (OTH)

AF:

0.000950

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.94

(source)

DANN

Benign

0.61

PhyloP100

-0.19

PromoterAI

-0.0046

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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