rs3024517

Positions:

• chr1-206866908-A-G

Variant summary

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

The NM_018724.4(IL20):​c.378+272A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,152 control chromosomes in the GnomAD database, including 2,257 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 0.16 (2257 hom., cov: 32)
• Consequence: IL20 NM_018724.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL20	NM_018724.4	c.378+272A>G		intron_variant		ENST00000367098.6
IL20	NM_001385165.1	c.378+272A>G		intron_variant
IL20	NM_001385166.1	c.378+272A>G		intron_variant
IL20	NM_001385167.1	c.378+272A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL20	ENST00000367098.6	c.378+272A>G		intron_variant		1	NM_018724.4	P1
IL20	ENST00000367096.7	c.378+272A>G		intron_variant		1		P1
IL20	ENST00000391930.3	c.378+272A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24823 AN: 152034 Hom.: 2247 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.163 AC: 24858 AN: 152152 Hom.: 2257 Cov.: 32 AF XY: 0.166 AC XY: 12315 AN XY: 74400

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.117

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.178

Alfa AF: 0.149 Hom.: 262

Bravo AF: 0.168

Asia WGS AF: 0.271 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.69

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: rs3024517; hg19: chr1-207040253;