rs3024523

Variant names:

• chr1-206869339-T-C
• rs3024523
• NM_018724.4:c.*775T>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.*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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018724.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20	NM_018724.4	MANE Select	c.*775T>C		downstream_gene	N/A	NP_061194.2
	IL20	NM_001385166.1		c.*775T>C		downstream_gene	N/A	NP_001372095.1	Q9NYY1-1
	IL20	NM_001385167.1		c.*775T>C		downstream_gene	N/A	NP_001372096.1	Q9NYY1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20	ENST00000367098.6	TSL:1 MANE Select	c.*775T>C		downstream_gene	N/A	ENSP00000356065.1	Q9NYY1-1
	IL20	ENST00000391930.3	TSL:1	c.*775T>C		downstream_gene	N/A	ENSP00000375796.2	Q9NYY1-2

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8403 AN: 152014 Hom.: 415 Cov.: 32

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: 2 AN: 156 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 94

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.0149 AC: 2 AN: 134

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 14

Other (OTH) AF: 0.00 AC: 0 AN: 6

GnomAD4 genome AF: 0.0555 AC: 8438 AN: 152132 Hom.: 422 Cov.: 32 AF XY: 0.0539 AC XY: 4013 AN XY: 74394

African (AFR) AF: 0.128 AC: 5300 AN: 41454

American (AMR) AF: 0.0353 AC: 539 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0259 AC: 90 AN: 3470

East Asian (EAS) AF: 0.0382 AC: 198 AN: 5180

South Asian (SAS) AF: 0.0349 AC: 168 AN: 4820

European-Finnish (FIN) AF: 0.0267 AC: 283 AN: 10608

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0256 AC: 1744 AN: 68006

Other (OTH) AF: 0.0498 AC: 105 AN: 2108

Alfa AF: 0.0425 Hom.: 407

Bravo AF: 0.0618

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3024523; hg19: chr1-207042684;