chr6-137019467-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4	c.89-2364G>A		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.89-2364G>A		intron_variant	Intron 1 of 6	1	NM_014432.4	ENSP00000314976.5

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

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.909

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.572

Alfa AF: 0.620 Hom.: 7173

Bravo AF: 0.553

Asia WGS AF: 0.649 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.75

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

Publications

LitVar

Other links and lift over

dbSNP: rs1184860; hg19: chr6-137340604;