dbSNP rs3024523: IL20:c.*775T>C (chr1-206869339-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018724.4(IL20):c.*775T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0554 in 152,288 control chromosomes in the GnomAD database, including 422 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 0.055 ( 422 hom., cov: 32)

Exomes 𝑓: 0.013 ( 0 hom. )

Consequence

IL20
NM_018724.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
IL20	NM_018724.4 link	c.*775T>C	downstream_gene_variant	ENST00000367098.6	NP_061194.2	Q9NYY1-1A0A7R8C4W0
IL20	NM_001385166.1 link	c.*775T>C	downstream_gene_variant		NP_001372095.1
IL20	NM_001385167.1 link	c.*775T>C	downstream_gene_variant		NP_001372096.1
IL20	NM_001385165.1 link	c.*775T>C	downstream_gene_variant		NP_001372094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20	ENST00000367098.6 link	c.*775T>C		downstream_gene_variant		1	NM_018724.4	ENSP00000356065.1		Q9NYY1-1
IL20	ENST00000391930.3 link	c.*775T>C		downstream_gene_variant		1		ENSP00000375796.2		Q9NYY1-2

Frequencies

GnomAD3 genomes

AF:

0.0553

AC:

8403

AN:

152014

Hom.:

415

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.0353

Gnomad ASJ

AF:

0.0259

Gnomad EAS

AF:

0.0381

Gnomad SAS

AF:

0.0348

Gnomad FIN

AF:

0.0267

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0257

Gnomad OTH

AF:

0.0503

GnomAD4 exome

AF:

0.0128

AC:

AN:

156

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 EAS exome

AF:

0.0149

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0555

AC:

8438

AN:

152132

Hom.:

422

Cov.:

AF XY:

0.0539

AC XY:

4013

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.128

Gnomad4 AMR

AF:

0.0353

Gnomad4 ASJ

AF:

0.0259

Gnomad4 EAS

AF:

0.0382

Gnomad4 SAS

AF:

0.0349

Gnomad4 FIN

AF:

0.0267

Gnomad4 NFE

AF:

0.0256

Gnomad4 OTH

AF:

0.0498

Alfa

AF:

0.0587

Hom.:

Bravo

AF:

0.0618

Asia WGS

AF:

0.0430

AC:

149

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

DANN

Benign

0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over