6-137014470-A-G

Variant names:

• chr6-137014470-A-G
• rs1322394
• NM_014432.4:c.224+2498T>C

Variant summary

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

The NM_014432.4(IL20RA):​c.224+2498T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,050 control chromosomes in the GnomAD database, including 34,569 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 0.63 (34569 hom., cov: 31)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• 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=-0.9).
• 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.224+2498T>C		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.224+2498T>C		intron_variant	Intron 2 of 6	1	NM_014432.4	ENSP00000314976.5

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95085 AN: 151932 Hom.: 34578 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.764

Gnomad OTH AF: 0.630

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

GnomAD4 genome AF: 0.625 AC: 95090 AN: 152050 Hom.: 34569 Cov.: 31 AF XY: 0.637 AC XY: 47331 AN XY: 74346

African (AFR) AF: 0.226 AC: 9373 AN: 41448

American (AMR) AF: 0.754 AC: 11521 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2611 AN: 3464

East Asian (EAS) AF: 0.932 AC: 4834 AN: 5184

South Asian (SAS) AF: 0.798 AC: 3844 AN: 4816

European-Finnish (FIN) AF: 0.828 AC: 8745 AN: 10566

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.764 AC: 51909 AN: 67974

Other (OTH) AF: 0.630 AC: 1331 AN: 2114

Alfa AF: 0.733 Hom.: 26352

Bravo AF: 0.604

Asia WGS AF: 0.764 AC: 2648 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.037
DANN	Benign	0.55
PhyloP100		-2.9
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: rs1322394; hg19: chr6-137335607;