Genetic Variant NM_001319.7:c.448-25C>T (chr19-1978834-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.448-25C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0199 in 1,592,444 control chromosomes in the GnomAD database, including 428 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 0.017 ( 51 hom., cov: 31)

Exomes 𝑓: 0.020 ( 377 hom. )

Consequence

CSNK1G2
NM_001319.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.870

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=-0.85).

BA1

GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK1G2	NM_001319.7 link	c.448-25C>T		intron_variant	Intron 5 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.448-25C>T		intron_variant	Intron 5 of 11	1	NM_001319.7	ENSP00000255641.7		P78368

Frequencies

GnomAD3 genomes

AF:

0.0171

AC:

2585

AN:

151536

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0352

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.0470

Gnomad SAS

AF:

0.0220

Gnomad FIN

AF:

0.0168

Gnomad MID

AF:

0.00323

Gnomad NFE

AF:

0.0172

Gnomad OTH

AF:

0.0139

GnomAD2 exomes

AF:

0.0275

AC:

6134

AN:

222906

AF XY:

0.0248

show subpopulations

Gnomad AFR exome

AF:

0.00710

Gnomad AMR exome

AF:

0.0754

Gnomad ASJ exome

AF:

0.00397

Gnomad EAS exome

AF:

0.0431

Gnomad FIN exome

AF:

0.0204

Gnomad NFE exome

AF:

0.0180

Gnomad OTH exome

AF:

0.0273

GnomAD4 exome

AF:

0.0202

AC:

29137

AN:

1440788

Hom.:

377

Cov.:

AF XY:

0.0199

AC XY:

14245

AN XY:

716006

show subpopulations

African (AFR)

AF:

0.00727

AC:

241

AN:

33148

American (AMR)

AF:

0.0697

AC:

3033

AN:

43528

Ashkenazi Jewish (ASJ)

AF:

0.00431

AC:

109

AN:

25288

East Asian (EAS)

AF:

0.0371

AC:

1466

AN:

39474

South Asian (SAS)

AF:

0.0186

AC:

1580

AN:

85082

European-Finnish (FIN)

AF:

0.0215

AC:

948

AN:

44144

Middle Eastern (MID)

AF:

0.00598

AC:

AN:

5688

European-Non Finnish (NFE)

AF:

0.0187

AC:

20691

AN:

1104670

Other (OTH)

AF:

0.0173

AC:

1035

AN:

59766

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1750

3500

5251

7001

8751

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

858

1716

2574

3432

4290

<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:

0.0171

AC:

2590

AN:

151656

Hom.:

Cov.:

AF XY:

0.0177

AC XY:

1314

AN XY:

74104

show subpopulations

African (AFR)

AF:

0.00746

AC:

308

AN:

41302

American (AMR)

AF:

0.0354

AC:

540

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.00519

AC:

AN:

3470

East Asian (EAS)

AF:

0.0477

AC:

243

AN:

5090

South Asian (SAS)

AF:

0.0216

AC:

104

AN:

4804

European-Finnish (FIN)

AF:

0.0168

AC:

177

AN:

10564

Middle Eastern (MID)

AF:

0.00347

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.0172

AC:

1169

AN:

67856

Other (OTH)

AF:

0.0142

AC:

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

123

246

369

492

615

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

128

160

<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:

0.0153

Hom.:

Bravo

AF:

0.0193

Asia WGS

AF:

0.0270

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.80

(source)

DANN

Benign

0.58

PhyloP100

-0.87

PromoterAI

-0.021

Neutral

(source)

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.3

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