Variant chr6-137002076-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014432.4(IL20RA):c.1144C>T(p.Leu382Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 1,613,872 control chromosomes in the GnomAD database, including 50,866 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.23 ( 4096 hom., cov: 32)

Exomes 𝑓: 0.25 ( 46770 hom. )

Consequence

IL20RA
NM_014432.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

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 Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005023539).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL20RA	NM_014432.4 linkuse as main transcript	c.1144C>T	p.Leu382Phe	missense_variant	7/7	ENST00000316649.10	NP_055247.4	Q9UHF4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IL20RA	ENST00000316649.10 linkuse as main transcript	c.1144C>T	p.Leu382Phe	missense_variant	7/7	1	NM_014432.4	ENSP00000314976.5	Q9UHF4-1
IL20RA	ENST00000367748.4 linkuse as main transcript	c.811C>T	p.Leu271Phe	missense_variant	6/6	1		ENSP00000356722.1	Q9UHF4-2
IL20RA	ENST00000541547.5 linkuse as main transcript	c.997C>T	p.Leu333Phe	missense_variant	7/7	2		ENSP00000437843.1	Q9UHF4-3

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34489

AN:

151948

Hom.:

4091

Cov.:

show subpopulations

Gnomad AFR

AF:

0.215

Gnomad AMI

AF:

0.275

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.0668

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.178

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.261

Gnomad OTH

AF:

0.256

GnomAD3 exomes

AF:

0.216

AC:

54356

AN:

251316

Hom.:

6494

AF XY:

0.222

AC XY:

30206

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.217

Gnomad AMR exome

AF:

0.140

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.0660

Gnomad SAS exome

AF:

0.238

Gnomad FIN exome

AF:

0.181

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.249

AC:

364025

AN:

1461806

Hom.:

46770

Cov.:

AF XY:

0.250

AC XY:

181522

AN XY:

727214

show subpopulations

Gnomad4 AFR exome

AF:

0.217

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.226

Gnomad4 EAS exome

AF:

0.0675

Gnomad4 SAS exome

AF:

0.232

Gnomad4 FIN exome

AF:

0.185

Gnomad4 NFE exome

AF:

0.266

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.227

AC:

34517

AN:

152066

Hom.:

4096

Cov.:

AF XY:

0.220

AC XY:

16371

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.215

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.0672

Gnomad4 SAS

AF:

0.217

Gnomad4 FIN

AF:

0.178

Gnomad4 NFE

AF:

0.261

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.253

Hom.:

11622

Bravo

AF:

0.226

TwinsUK

AF:

0.258

AC:

955

ALSPAC

AF:

0.260

AC:

1001

ESP6500AA

AF:

0.222

AC:

977

ESP6500EA

AF:

0.270

AC:

2322

ExAC

AF:

0.221

AC:

26865

Asia WGS

AF:

0.191

AC:

668

AN:

3478

EpiCase

AF:

0.262

EpiControl

AF:

0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.67

BayesDel_noAF

Benign

-0.59

CADD

Benign

8.6

DANN

Uncertain

0.99

DEOGEN2

Benign

0.014

.;T;.

Eigen

Benign

-0.40

Eigen_PC

Benign

-0.58

FATHMM_MKL

Benign

0.13

LIST_S2

Benign

0.56

T;T;T

MetaRNN

Benign

0.0050

T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.8

.;L;.

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.6

N;N;N

REVEL

Benign

0.068

Sift

Benign

0.078

T;T;T

Sift4G

Benign

0.13

T;T;T

Polyphen

0.93, 0.90

.;P;P

Vest4

0.038

MPC

0.50

ClinPred

0.013

GERP RS

0.25

Varity_R

0.049

gMVP

0.16

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

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