6-137027888-A-G

Variant names:

• chr6-137027888-A-G
• rs1167849
• NM_014432.4:c.89-10785T>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.89-10785T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,186 control chromosomes in the GnomAD database, including 30,574 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 0.58 (30574 hom., cov: 32)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.798
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.89-10785T>C		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.89-10785T>C		intron_variant	Intron 1 of 6	1	NM_014432.4	ENSP00000314976.5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87624 AN: 152068 Hom.: 30574 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.728

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.576 AC: 87619 AN: 152186 Hom.: 30574 Cov.: 32 AF XY: 0.584 AC XY: 43482 AN XY: 74396

African (AFR) AF: 0.160 AC: 6629 AN: 41512

American (AMR) AF: 0.728 AC: 11141 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4706 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2846 AN: 4830

European-Finnish (FIN) AF: 0.804 AC: 8502 AN: 10580

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49383 AN: 67998

Other (OTH) AF: 0.576 AC: 1217 AN: 2114

Alfa AF: 0.675 Hom.: 46488

Bravo AF: 0.557

Asia WGS AF: 0.652 AC: 2266 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	13
DANN	Benign	0.80
PhyloP100		0.80
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: rs1167849; hg19: chr6-137349025;