Genetic Variant IL20RA:c.725-5dupT (chr6-137004764-T-TA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_014432.4(IL20RA):c.725-5dupT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 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 0.046 ( 498 hom., cov: 0)

Exomes 𝑓: 0.0046 ( 2 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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

AF:

0.0457

AC:

6666

AN:

145978

Hom.:

497

Cov.:

show subpopulations

Gnomad AFR

AF:

0.162

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0141

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000215

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.000764

Gnomad OTH

AF:

0.0312

GnomAD2 exomes

AF:

0.0126

AC:

1913

AN:

151602

AF XY:

0.00949

show subpopulations

Gnomad AFR exome

AF:

0.148

Gnomad AMR exome

AF:

0.00801

Gnomad ASJ exome

AF:

0.000898

Gnomad EAS exome

AF:

0.0000990

Gnomad FIN exome

AF:

0.0000806

Gnomad NFE exome

AF:

0.000949

Gnomad OTH exome

AF:

0.00463

GnomAD4 exome

AF:

0.00456

AC:

5904

AN:

1294468

Hom.:

Cov.:

AF XY:

0.00416

AC XY:

2682

AN XY:

645320

show subpopulations

Gnomad4 AFR exome

AF:

0.152

AC:

4251

AN:

27896

Gnomad4 AMR exome

AF:

0.00753

AC:

214

AN:

28432

Gnomad4 ASJ exome

AF:

0.000676

AC:

AN:

22196

Gnomad4 EAS exome

AF:

0.000164

AC:

AN:

36670

Gnomad4 SAS exome

AF:

0.000881

AC:

AN:

72664

Gnomad4 FIN exome

AF:

0.000138

AC:

AN:

43556

Gnomad4 NFE exome

AF:

0.000814

AC:

818

AN:

1004628

Gnomad4 Remaining exome

AF:

0.00906

AC:

486

AN:

53632

Heterozygous variant carriers

292

584

876

1168

1460

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

168

336

504

672

840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0458

AC:

6685

AN:

146026

Hom.:

498

Cov.:

AF XY:

0.0444

AC XY:

3144

AN XY:

70880

show subpopulations

Gnomad4 AFR

AF:

0.162

AC:

0.162128

AN:

0.162128

Gnomad4 AMR

AF:

0.0141

AC:

0.0140893

AN:

0.0140893

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000216

AC:

0.000215889

AN:

0.000215889

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000764

AC:

0.000764251

AN:

0.000764251

Gnomad4 OTH

AF:

0.0310

AC:

0.0309735

AN:

0.0309735

Heterozygous variant carriers

252

504

756

1008

1260

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

132

198

264

330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Mutation Taster

=99/1

polymorphism (auto)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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