NM_014432.4:c.89-8887T>C

Variant names:

• chr6-137025990-A-G
• rs276497
• NM_014432.4:c.89-8887T>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.89-8887T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.821 in 152,220 control chromosomes in the GnomAD database, including 56,613 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 0.82 (56613 hom., cov: 33)
• Consequence: IL20RA NM_014432.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.988 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	NM_014432.4	MANE Select	c.89-8887T>C		intron	N/A	NP_055247.4
	IL20RA	NM_001278722.2		c.-59-8887T>C		intron	N/A	NP_001265651.2
	IL20RA	NM_001278723.3		c.-66-8887T>C		intron	N/A	NP_001265652.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL20RA	ENST00000316649.10	TSL:1 MANE Select	c.89-8887T>C		intron	N/A	ENSP00000314976.5
	IL20RA	ENST00000367748.4	TSL:1	c.-66-8887T>C		intron	N/A	ENSP00000356722.1
	IL20RA	ENST00000541547.5	TSL:2	c.-59-8887T>C		intron	N/A	ENSP00000437843.1

Frequencies

GnomAD3 genomes AF: 0.821 AC: 124911 AN: 152102 Hom.: 56606 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.994

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.821 AC: 124948 AN: 152220 Hom.: 56613 Cov.: 33 AF XY: 0.827 AC XY: 61528 AN XY: 74434

African (AFR) AF: 0.396 AC: 16428 AN: 41464

American (AMR) AF: 0.917 AC: 14029 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.950 AC: 3297 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5175 AN: 5176

South Asian (SAS) AF: 0.995 AC: 4804 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10626 AN: 10628

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67611 AN: 68028

Other (OTH) AF: 0.847 AC: 1793 AN: 2116

Alfa AF: 0.873 Hom.: 7906

Bravo AF: 0.794

Asia WGS AF: 0.965 AC: 3356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.040
DANN	Benign	0.59
PhyloP100		-2.0
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: rs276497; hg19: chr6-137347127;