6-137013809-C-A

Variant names:

• chr6-137013809-C-A
• rs1322393
• NM_014432.4:c.225-2357G>T

Variant summary

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

The NM_014432.4(IL20RA):​c.225-2357G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,056 control chromosomes in the GnomAD database, including 32,883 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 0.61 (32883 hom., cov: 31)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 7 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.225-2357G>T		intron_variant	Intron 2 of 6	ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.225-2357G>T		intron_variant	Intron 2 of 6	1	NM_014432.4	ENSP00000314976.5

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92827 AN: 151938 Hom.: 32891 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.739

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.610 AC: 92830 AN: 152056 Hom.: 32883 Cov.: 31 AF XY: 0.622 AC XY: 46260 AN XY: 74328

African (AFR) AF: 0.224 AC: 9280 AN: 41482

American (AMR) AF: 0.741 AC: 11335 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2577 AN: 3466

East Asian (EAS) AF: 0.934 AC: 4819 AN: 5160

South Asian (SAS) AF: 0.791 AC: 3808 AN: 4812

European-Finnish (FIN) AF: 0.815 AC: 8604 AN: 10560

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

European-Non Finnish (NFE) AF: 0.739 AC: 50199 AN: 67968

Other (OTH) AF: 0.615 AC: 1296 AN: 2108

Alfa AF: 0.698 Hom.: 26711

Bravo AF: 0.589

Asia WGS AF: 0.761 AC: 2643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.5
DANN	Benign	0.82
PhyloP100		-0.84
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: rs1322393; hg19: chr6-137334946;