1-206864130-G-C

Variant names:

• chr1-206864130-G-C
• rs1713239
• NM_001385166.1:c.-171+523G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001385166.1(IL20):​c.-171+523G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 152,152 control chromosomes in the GnomAD database, including 58,225 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 0.87 (58225 hom., cov: 30)
• Consequence: IL20 NM_001385166.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 12 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20	NM_001385166.1	c.-171+523G>C		intron_variant	Intron 1 of 6		NP_001372095.1
IL20	NM_001385167.1	c.-252+523G>C		intron_variant	Intron 1 of 7		NP_001372096.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132531 AN: 152034 Hom.: 58171 Cov.: 30

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.858

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.857

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.872 AC: 132640 AN: 152152 Hom.: 58225 Cov.: 30 AF XY: 0.866 AC XY: 64377 AN XY: 74374

African (AFR) AF: 0.961 AC: 39887 AN: 41524

American (AMR) AF: 0.798 AC: 12197 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3148 AN: 3466

East Asian (EAS) AF: 0.657 AC: 3407 AN: 5182

South Asian (SAS) AF: 0.777 AC: 3739 AN: 4814

European-Finnish (FIN) AF: 0.823 AC: 8694 AN: 10564

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58717 AN: 68012

Other (OTH) AF: 0.858 AC: 1810 AN: 2110

Alfa AF: 0.873 Hom.: 7291

Bravo AF: 0.873

Asia WGS AF: 0.765 AC: 2659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.38
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs1713239; hg19: chr1-207037475; COSMIC: COSV65584356;