Genetic Variant NM_018724.4:c.454-29C>T (chr1-206868458-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_018724.4(IL20):c.454-29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,546,054 control chromosomes in the GnomAD database, including 2,818 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 0.078 ( 1535 hom., cov: 32)

Exomes 𝑓: 0.0087 ( 1283 hom. )

Consequence

IL20
NM_018724.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.03

Publications

8 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=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IL20	NM_018724.4 link	c.454-29C>T	intron_variant	Intron 5 of 5	ENST00000367098.6	NP_061194.2	Q9NYY1-1A0A7R8C4W0
IL20	NM_001385166.1 link	c.454-29C>T	intron_variant	Intron 6 of 6		NP_001372095.1
IL20	NM_001385167.1 link	c.454-29C>T	intron_variant	Intron 7 of 7		NP_001372096.1
IL20	NM_001385165.1 link	c.379-29C>T	intron_variant	Intron 4 of 4		NP_001372094.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL20	ENST00000367098.6 link	c.454-29C>T	intron_variant	Intron 5 of 5	1	NM_018724.4	ENSP00000356065.1	Q9NYY1-1
IL20	ENST00000367096.7 link	c.454-29C>T	intron_variant	Intron 4 of 4	1		ENSP00000356063.3	Q9NYY1-1
IL20	ENST00000391930.3 link	c.379-29C>T	intron_variant	Intron 3 of 3	1		ENSP00000375796.2	Q9NYY1-2

Frequencies

GnomAD3 genomes

AF:

0.0777

AC:

11817

AN:

152078

Hom.:

1531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.268

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0312

Gnomad ASJ

AF:

0.00461

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00190

Gnomad OTH

AF:

0.0554

GnomAD2 exomes

AF:

0.0202

AC:

4321

AN:

213508

AF XY:

0.0147

show subpopulations

Gnomad AFR exome

AF:

0.274

Gnomad AMR exome

AF:

0.0154

Gnomad ASJ exome

AF:

0.00357

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00191

Gnomad OTH exome

AF:

0.0121

GnomAD4 exome

AF:

0.00873

AC:

12169

AN:

1393858

Hom.:

1283

Cov.:

AF XY:

0.00767

AC XY:

5317

AN XY:

692808

show subpopulations

African (AFR)

AF:

0.279

AC:

8525

AN:

30510

American (AMR)

AF:

0.0180

AC:

680

AN:

37820

Ashkenazi Jewish (ASJ)

AF:

0.00301

AC:

AN:

24578

East Asian (EAS)

AF:

0.0000560

AC:

AN:

35732

South Asian (SAS)

AF:

0.000702

AC:

AN:

76972

European-Finnish (FIN)

AF:

0.0000575

AC:

AN:

52146

Middle Eastern (MID)

AF:

0.0283

AC:

158

AN:

5584

European-Non Finnish (NFE)

AF:

0.00142

AC:

1527

AN:

1073208

Other (OTH)

AF:

0.0200

AC:

1146

AN:

57308

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

438

875

1313

1750

2188

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.0778

AC:

11839

AN:

152196

Hom.:

1535

Cov.:

AF XY:

0.0752

AC XY:

5597

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.267

AC:

11082

AN:

41446

American (AMR)

AF:

0.0312

AC:

477

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.00461

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.00166

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00190

AC:

129

AN:

68030

Other (OTH)

AF:

0.0548

AC:

116

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

452

904

1356

1808

2260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

106

212

318

424

530

<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:

0.0311

Hom.:

659

Bravo

AF:

0.0882

Asia WGS

AF:

0.0200

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

(source)

DANN

Benign

0.55

PhyloP100

2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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