rs1167846

Variant names:

• chr6-137022583-T-C
• rs1167846
• NM_014432.4:c.89-5480A>G

Variant summary

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

The NM_014432.4(IL20RA):​c.89-5480A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,092 control chromosomes in the GnomAD database, including 34,192 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 0.62 (34192 hom., cov: 31)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 3 publications found

Genes affected

IL20RA (HGNC:6003): (interleukin 20 receptor subunit alpha) This gene encodes a member of the type II cytokine receptor family. The encoded protein is a subunit of the receptor for interleukin 20, a cytokine that may be involved in epidermal function. The interleukin 20 receptor is a heterodimeric complex consisting of the encoded protein and interleukin 20 receptor beta. This gene and interleukin 20 receptor beta are highly expressed in skin, and are upregulated in psoriasis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.89-5480A>G		intron_variant	Intron 1 of 6	ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.89-5480A>G		intron_variant	Intron 1 of 6	1	NM_014432.4	ENSP00000314976.5

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94509 AN: 151974 Hom.: 34189 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.622 AC: 94529 AN: 152092 Hom.: 34192 Cov.: 31 AF XY: 0.633 AC XY: 47033 AN XY: 74348

African (AFR) AF: 0.225 AC: 9331 AN: 41486

American (AMR) AF: 0.752 AC: 11493 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2529 AN: 3468

East Asian (EAS) AF: 0.933 AC: 4841 AN: 5188

South Asian (SAS) AF: 0.793 AC: 3825 AN: 4826

European-Finnish (FIN) AF: 0.823 AC: 8694 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51609 AN: 67964

Other (OTH) AF: 0.624 AC: 1316 AN: 2110

Alfa AF: 0.710 Hom.: 123012

Bravo AF: 0.598

Asia WGS AF: 0.791 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.43
PhyloP100		-0.78
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: rs1167846; hg19: chr6-137343720;