rs2232360

Variant names:

• chr1-206867314-G-A
• rs2232360
• NM_018724.4:c.379-70G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-206867314-G-A
• chr1-206867314-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IL20	NM_018724.4	c.379-70G>A		intron_variant	Intron 4 of 5	ENST00000367098.6	NP_061194.2
IL20	NM_001385166.1	c.379-70G>A		intron_variant	Intron 5 of 6		NP_001372095.1
IL20	NM_001385167.1	c.379-70G>A		intron_variant	Intron 6 of 7		NP_001372096.1
IL20	NM_001385165.1	c.378+678G>A		intron_variant	Intron 4 of 4		NP_001372094.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20	ENST00000367098.6	c.379-70G>A		intron_variant	Intron 4 of 5	1	NM_018724.4	ENSP00000356065.1
IL20	ENST00000367096.7	c.379-70G>A		intron_variant	Intron 3 of 4	1		ENSP00000356063.3
IL20	ENST00000391930.3	c.378+678G>A		intron_variant	Intron 3 of 3	1		ENSP00000375796.2

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

African (AFR) AF: 0.836 AC: 23692 AN: 28334

American (AMR) AF: 0.631 AC: 27327 AN: 43304

Ashkenazi Jewish (ASJ) AF: 0.828 AC: 19803 AN: 23928

East Asian (EAS) AF: 0.290 AC: 11025 AN: 38022

South Asian (SAS) AF: 0.698 AC: 55033 AN: 78848

European-Finnish (FIN) AF: 0.736 AC: 38429 AN: 52226

Middle Eastern (MID) AF: 0.730 AC: 3647 AN: 4996

European-Non Finnish (NFE) AF: 0.782 AC: 690990 AN: 883980

Other (OTH) AF: 0.749 AC: 38678 AN: 51626

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

African (AFR) AF: 0.825 AC: 34125 AN: 41340

American (AMR) AF: 0.690 AC: 10549 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2867 AN: 3472

East Asian (EAS) AF: 0.328 AC: 1693 AN: 5162

South Asian (SAS) AF: 0.695 AC: 3334 AN: 4800

European-Finnish (FIN) AF: 0.741 AC: 7825 AN: 10562

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53099 AN: 67974

Other (OTH) AF: 0.755 AC: 1591 AN: 2108

Alfa AF: 0.767 Hom.: 19841

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
PhyloP100		0.010
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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