rs2232360

chr1-206867314-G-Achr1-206867314-G-C

Variant summary

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

The NM_018724.4(IL20):c.379-70G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 1,357,168 control chromosomes in the GnomAD database, including 393,291 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 (45000 hom., cov: 30)
  • Exomes 𝑓: 0.75 (348291 hom.)
• Consequence: IL20 NM_018724.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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=-0.86).
• 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.379-70G>A		intron_variant		ENST00000367098.6
IL20	NM_001385165.1	c.378+678G>A		intron_variant
IL20	NM_001385166.1	c.379-70G>A		intron_variant
IL20	NM_001385167.1	c.379-70G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL20	ENST00000367098.6	c.379-70G>A		intron_variant		1	NM_018724.4	P1
IL20	ENST00000367096.7	c.379-70G>A		intron_variant		1		P1
IL20	ENST00000391930.3	c.378+678G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115911 AN: 151786 Hom.: 44944 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: 0.328

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.754 AC: 908624 AN: 1205264 Hom.: 348291 AF XY: 0.753 AC XY: 459016 AN XY: 609892

Gnomad4 AFR exome AF: 0.836

Gnomad4 AMR exome AF: 0.631

Gnomad4 ASJ exome AF: 0.828

Gnomad4 EAS exome AF: 0.290

Gnomad4 SAS exome AF: 0.698

Gnomad4 FIN exome AF: 0.736

Gnomad4 NFE exome AF: 0.782

Gnomad4 OTH exome AF: 0.749

GnomAD4 genome AF: 0.764 AC: 116020 AN: 151904 Hom.: 45000 Cov.: 30 AF XY: 0.757 AC XY: 56175 AN XY: 74240

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.826

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.755

Alfa AF: 0.765 Hom.: 17466

Bravo AF: 0.759

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.90
Dann	Benign	0.21

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: rs2232360; hg19: chr1-207040659; COSMIC: COSV65584371;