dbSNP rs2981573: 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:

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=-0.89).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
IL20	NM_018724.4 link	c.379-152G>A	intron_variant	Intron 4 of 5	ENST00000367098.6	NP_061194.2
IL20	NM_001385166.1 link	c.379-152G>A	intron_variant	Intron 5 of 6		NP_001372095.1
IL20	NM_001385167.1 link	c.379-152G>A	intron_variant	Intron 6 of 7		NP_001372096.1
IL20	NM_001385165.1 link	c.378+596G>A	intron_variant	Intron 4 of 4		NP_001372094.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
IL20	ENST00000367098.6 link	c.379-152G>A	intron_variant	Intron 4 of 5	1	NM_018724.4	ENSP00000356065.1
IL20	ENST00000367096.7 link	c.379-152G>A	intron_variant	Intron 3 of 4	1		ENSP00000356063.3
IL20	ENST00000391930.3 link	c.378+596G>A	intron_variant	Intron 3 of 3	1		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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over