Variant NM_014432.4:c.725-8_725-5delTTTT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_014432.4(IL20RA):c.725-8_725-5delTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00072 in 1,437,352 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000068 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00080 ( 0 hom. )

Consequence

IL20RA
NM_014432.4 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Variant links:

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]

IL20RA links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL20RA	NM_014432.4 link	c.725-8_725-5delTTTT		splice_region_variant, intron_variant	Intron 5 of 6	ENST00000316649.10	NP_055247.4	Q9UHF4-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL20RA	ENST00000316649.10 link	c.725-8_725-5delTTTT	splice_region_variant, intron_variant	Intron 5 of 6	1	NM_014432.4	ENSP00000314976.5	Q9UHF4-1
IL20RA	ENST00000367748.4 link	c.392-8_392-5delTTTT	splice_region_variant, intron_variant	Intron 4 of 5	1		ENSP00000356722.1	Q9UHF4-2
IL20RA	ENST00000541547.5 link	c.578-8_578-5delTTTT	splice_region_variant, intron_variant	Intron 5 of 6	2		ENSP00000437843.1	Q9UHF4-3
IL20RA	ENST00000468393.5 link	c.392-8_392-5delTTTT	splice_region_variant, intron_variant	Intron 4 of 4	4		ENSP00000489177.1	A0A0U1RQU9

Frequencies

GnomAD3 genomes

AF:

0.00000685

AC:

AN:

146030

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000113

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00191

AC:

289

AN:

151602

Hom.:

AF XY:

0.00197

AC XY:

165

AN XY:

83602

show subpopulations

Gnomad AFR exome

AF:

0.000176

Gnomad AMR exome

AF:

0.00254

Gnomad ASJ exome

AF:

0.00287

Gnomad EAS exome

AF:

0.00475

Gnomad SAS exome

AF:

0.00252

Gnomad FIN exome

AF:

0.00250

Gnomad NFE exome

AF:

0.00132

Gnomad OTH exome

AF:

0.00260

GnomAD4 exome

AF:

0.000801

AC:

1034

AN:

1291322

Hom.:

AF XY:

0.000833

AC XY:

536

AN XY:

643544

show subpopulations

Gnomad4 AFR exome

AF:

0.000140

Gnomad4 AMR exome

AF:

0.00237

Gnomad4 ASJ exome

AF:

0.00109

Gnomad4 EAS exome

AF:

0.00288

Gnomad4 SAS exome

AF:

0.00150

Gnomad4 FIN exome

AF:

0.00176

Gnomad4 NFE exome

AF:

0.000607

Gnomad4 OTH exome

AF:

0.000765

GnomAD4 genome

AF:

0.00000685

AC:

AN:

146030

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

70848

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000113

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over