rs2981573

chr1-206867232-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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]

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	#exon/exons	MANE	UniProt
IL20	NM_018724.4	c.379-152G>A		intron_variant		ENST00000367098.6
IL20	NM_001385165.1	c.378+596G>A		intron_variant
IL20	NM_001385166.1	c.379-152G>A		intron_variant
IL20	NM_001385167.1	c.379-152G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL20	ENST00000367098.6	c.379-152G>A		intron_variant		1	NM_018724.4	P1
IL20	ENST00000367096.7	c.379-152G>A		intron_variant		1		P1
IL20	ENST00000391930.3	c.378+596G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115994 AN: 151836 Hom.: 44984 Cov.: 30

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

Gnomad4 AFR exome AF: 0.833

Gnomad4 AMR exome AF: 0.651

Gnomad4 ASJ exome AF: 0.826

Gnomad4 EAS exome AF: 0.286

Gnomad4 SAS exome AF: 0.691

Gnomad4 FIN exome AF: 0.735

Gnomad4 NFE exome AF: 0.781

Gnomad4 OTH exome AF: 0.744

GnomAD4 genome AF: 0.764 AC: 116102 AN: 151954 Hom.: 45039 Cov.: 30 AF XY: 0.757 AC XY: 56214 AN XY: 74272

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.691

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.742

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.755

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
Dann	Benign	0.29

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

LitVar

Other links and lift over

dbSNP: rs2981573; hg19: chr1-207040577; COSMIC: COSV65584365;