Genetic Variant IL20:c.379-152G>A (chr1-206867232-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_018724.4(IL20):c.379-152G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.74 in 600,120 control chromosomes in the GnomAD database, including 169,114 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 0.76 ( 45039 hom., cov: 30)

Exomes 𝑓: 0.73 ( 124075 hom. )

Consequence

IL20
NM_018724.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.337

Publications

24 publications found

Variant links:

Genes affected

IL20 (HGNC:6002): (interleukin 20) The protein encoded by this gene is a cytokine structurally related to interleukin 10 (IL10). This cytokine has been shown to transduce its signal through signal transducer and activator of transcription 3 (STAT3) in keratinocytes. A specific receptor for this cytokine is found to be expressed in skin and upregulated dramatically in psoriatic skin, suggesting a role for this protein in epidermal function and psoriasis. [provided by RefSeq, Jul 2008]

IL20 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018724.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL20	NM_018724.4	MANE Select	c.379-152G>A	intron	N/A	NP_061194.2
IL20	NM_001385166.1		c.379-152G>A	intron	N/A	NP_001372095.1
IL20	NM_001385167.1		c.379-152G>A	intron	N/A	NP_001372096.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL20	ENST00000367098.6	TSL:1 MANE Select	c.379-152G>A	intron	N/A	ENSP00000356065.1
IL20	ENST00000367096.7	TSL:1	c.379-152G>A	intron	N/A	ENSP00000356063.3
IL20	ENST00000391930.3	TSL:1	c.378+596G>A	intron	N/A	ENSP00000375796.2

Frequencies

GnomAD3 genomes

AF:

0.764

AC:

115994

AN:

151836

Hom.:

44984

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.784

Gnomad AMR

AF:

0.691

Gnomad ASJ

AF:

0.826

Gnomad EAS

AF:

0.329

Gnomad SAS

AF:

0.695

Gnomad FIN

AF:

0.742

Gnomad MID

AF:

0.753

Gnomad NFE

AF:

0.781

Gnomad OTH

AF:

0.754

GnomAD4 exome

AF:

0.732

AC:

328076

AN:

448166

Hom.:

124075

AF XY:

0.731

AC XY:

171756

AN XY:

234830

show subpopulations

African (AFR)

AF:

0.833

AC:

10151

AN:

12188

American (AMR)

AF:

0.651

AC:

12363

AN:

19002

Ashkenazi Jewish (ASJ)

AF:

0.826

AC:

10694

AN:

12952

East Asian (EAS)

AF:

0.286

AC:

8506

AN:

29698

South Asian (SAS)

AF:

0.691

AC:

27452

AN:

39704

European-Finnish (FIN)

AF:

0.735

AC:

24917

AN:

33880

Middle Eastern (MID)

AF:

0.760

AC:

1444

AN:

1900

European-Non Finnish (NFE)

AF:

0.781

AC:

214169

AN:

274144

Other (OTH)

AF:

0.744

AC:

18380

AN:

24698

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

3710

7421

11131

14842

18552

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1438

2876

4314

5752

7190

<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:

0.764

AC:

116102

AN:

151954

Hom.:

45039

Cov.:

AF XY:

0.757

AC XY:

56214

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.826

AC:

34189

AN:

41402

American (AMR)

AF:

0.691

AC:

10544

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.826

AC:

2867

AN:

3472

East Asian (EAS)

AF:

0.328

AC:

1697

AN:

5170

South Asian (SAS)

AF:

0.695

AC:

3344

AN:

4810

European-Finnish (FIN)

AF:

0.742

AC:

7821

AN:

10538

Middle Eastern (MID)

AF:

0.755

AC:

222

AN:

294

European-Non Finnish (NFE)

AF:

0.781

AC:

53112

AN:

67980

Other (OTH)

AF:

0.755

AC:

1591

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1328

2656

3984

5312

6640

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.769

Hom.:

8084

Bravo

AF:

0.759

Asia WGS

AF:

0.568

AC:

1973

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.52

(source)

DANN

Benign

0.29

PhyloP100

-0.34

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