6-137027888-A-G

Position:

• chr6-137027888-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.89-10785T>C		intron_variant		ENST00000316649.10	NP_055247.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL20RA	ENST00000316649.10	c.89-10785T>C		intron_variant		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

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.728

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.910

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.576

Alfa AF: 0.698 Hom.: 36766

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs1167849; hg19: chr6-137349025;