6-137019467-C-T

Variant names:

• chr6-137019467-C-T
• rs1184860
• NM_014432.4:c.89-2364G>A

Variant summary

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

The NM_014432.4(IL20RA):​c.89-2364G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,974 control chromosomes in the GnomAD database, including 30,426 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 0.57 (30426 hom., cov: 31)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014432.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	NM_014432.4	MANE Select	c.89-2364G>A		intron	N/A	NP_055247.4
	IL20RA	NM_001278722.2		c.-59-2364G>A		intron	N/A	NP_001265651.2	Q9UHF4-3
	IL20RA	NM_001278723.3		c.-66-2364G>A		intron	N/A	NP_001265652.2	Q9UHF4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	ENST00000316649.10	TSL:1 MANE Select	c.89-2364G>A		intron	N/A	ENSP00000314976.5	Q9UHF4-1
	IL20RA	ENST00000367748.4	TSL:1	c.-66-2364G>A		intron	N/A	ENSP00000356722.1	Q9UHF4-2
	IL20RA	ENST00000878901.1		c.89-2364G>A		intron	N/A	ENSP00000548960.1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86994 AN: 151854 Hom.: 30427 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.572 AC: 86989 AN: 151974 Hom.: 30426 Cov.: 31 AF XY: 0.581 AC XY: 43186 AN XY: 74284

African (AFR) AF: 0.148 AC: 6131 AN: 41424

American (AMR) AF: 0.727 AC: 11110 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2341 AN: 3468

East Asian (EAS) AF: 0.909 AC: 4699 AN: 5172

South Asian (SAS) AF: 0.588 AC: 2831 AN: 4812

European-Finnish (FIN) AF: 0.803 AC: 8485 AN: 10564

Middle Eastern (MID) AF: 0.630 AC: 184 AN: 292

European-Non Finnish (NFE) AF: 0.726 AC: 49341 AN: 67944

Other (OTH) AF: 0.572 AC: 1210 AN: 2114

Alfa AF: 0.632 Hom.: 13132

Bravo AF: 0.553

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.75
PhyloP100		-0.31
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: rs1184860; hg19: chr6-137340604;