NM_018724.4:c.454-29C>T

Variant names:

• chr1-206868458-C-T
• rs1109461
• NM_018724.4:c.454-29C>T

Variant summary

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

The NM_018724.4(IL20):​c.454-29C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 1,546,054 control chromosomes in the GnomAD database, including 2,818 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 0.078 (1535 hom., cov: 32)
  • Exomes 𝑓: 0.0087 (1283 hom.)
• Consequence: IL20 NM_018724.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 8 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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.454-29C>T		intron	N/A	NP_061194.2
	IL20	NM_001385166.1		c.454-29C>T		intron	N/A	NP_001372095.1
	IL20	NM_001385167.1		c.454-29C>T		intron	N/A	NP_001372096.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20	ENST00000367098.6	TSL:1 MANE Select	c.454-29C>T		intron	N/A	ENSP00000356065.1
	IL20	ENST00000367096.7	TSL:1	c.454-29C>T		intron	N/A	ENSP00000356063.3
	IL20	ENST00000391930.3	TSL:1	c.379-29C>T		intron	N/A	ENSP00000375796.2

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11817 AN: 152078 Hom.: 1531 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00166

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.00190

Gnomad OTH AF: 0.0554

GnomAD2 exomes AF: 0.0202 AC: 4321 AN: 213508 AF XY: 0.0147

Gnomad AFR exome AF: 0.274

Gnomad AMR exome AF: 0.0154

Gnomad ASJ exome AF: 0.00357

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00191

Gnomad OTH exome AF: 0.0121

GnomAD4 exome AF: 0.00873 AC: 12169 AN: 1393858 Hom.: 1283 Cov.: 26 AF XY: 0.00767 AC XY: 5317 AN XY: 692808

African (AFR) AF: 0.279 AC: 8525 AN: 30510

American (AMR) AF: 0.0180 AC: 680 AN: 37820

Ashkenazi Jewish (ASJ) AF: 0.00301 AC: 74 AN: 24578

East Asian (EAS) AF: 0.0000560 AC: 2 AN: 35732

South Asian (SAS) AF: 0.000702 AC: 54 AN: 76972

European-Finnish (FIN) AF: 0.0000575 AC: 3 AN: 52146

Middle Eastern (MID) AF: 0.0283 AC: 158 AN: 5584

European-Non Finnish (NFE) AF: 0.00142 AC: 1527 AN: 1073208

Other (OTH) AF: 0.0200 AC: 1146 AN: 57308

GnomAD4 genome AF: 0.0778 AC: 11839 AN: 152196 Hom.: 1535 Cov.: 32 AF XY: 0.0752 AC XY: 5597 AN XY: 74426

African (AFR) AF: 0.267 AC: 11082 AN: 41446

American (AMR) AF: 0.0312 AC: 477 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00166 AC: 8 AN: 4826

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10622

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.00190 AC: 129 AN: 68030

Other (OTH) AF: 0.0548 AC: 116 AN: 2116

Alfa AF: 0.0311 Hom.: 659

Bravo AF: 0.0882

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.55
PhyloP100		2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1109461; hg19: chr1-207041803;