Variant rs9632389 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_139017.7(IL31RA):c.1449T>G(p.Gly483=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,613,758 control chromosomes in the GnomAD database, including 21,393 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1609 hom., cov: 32)

Exomes 𝑓: 0.16 ( 19784 hom. )

Consequence

IL31RA
NM_139017.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.612

Variant links:

Genes affected

IL31RA (HGNC:18969): (interleukin 31 receptor A) The protein encoded by this gene belongs to the type I cytokine receptor family. This receptor, with homology to gp130, is expressed on monocytes, and is involved in IL-31 signaling via activation of STAT-3 and STAT-5. It functions either as a monomer, or as part of a receptor complex with oncostatin M receptor (OSMR). Several alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]

IL31RA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 5-55908359-T-G is Benign according to our data. Variant chr5-55908359-T-G is described in ClinVar as [Benign]. Clinvar id is 1098854.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.612 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL31RA	NM_139017.7 linkuse as main transcript	c.1449T>G	p.Gly483=	synonymous_variant	11/15	ENST00000652347.2	NP_620586.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL31RA	ENST00000652347.2 linkuse as main transcript	c.1449T>G	p.Gly483=	synonymous_variant	11/15		NM_139017.7	ENSP00000498630	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19911

AN:

151764

Hom.:

1610

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0543

Gnomad AMI

AF:

0.0989

Gnomad AMR

AF:

0.127

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.00696

Gnomad SAS

AF:

0.106

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.241

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.135

AC:

34054

AN:

251436

Hom.:

2734

AF XY:

0.139

AC XY:

18931

AN XY:

135886

show subpopulations

Gnomad AFR exome

AF:

0.0533

Gnomad AMR exome

AF:

0.0910

Gnomad ASJ exome

AF:

0.167

Gnomad EAS exome

AF:

0.00190

Gnomad SAS exome

AF:

0.117

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.172

Gnomad OTH exome

AF:

0.163

GnomAD4 exome

AF:

0.160

AC:

233619

AN:

1461876

Hom.:

19784

Cov.:

AF XY:

0.159

AC XY:

115645

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.0514

Gnomad4 AMR exome

AF:

0.0930

Gnomad4 ASJ exome

AF:

0.174

Gnomad4 EAS exome

AF:

0.00897

Gnomad4 SAS exome

AF:

0.117

Gnomad4 FIN exome

AF:

0.191

Gnomad4 NFE exome

AF:

0.173

Gnomad4 OTH exome

AF:

0.155

GnomAD4 genome

AF:

0.131

AC:

19913

AN:

151882

Hom.:

1609

Cov.:

AF XY:

0.131

AC XY:

9738

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.0544

Gnomad4 AMR

AF:

0.127

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.00697

Gnomad4 SAS

AF:

0.105

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.146

Alfa

AF:

0.161

Hom.:

3453

Bravo

AF:

0.121

Asia WGS

AF:

0.0650

AC:

227

AN:

3478

EpiCase

AF:

0.180

EpiControl

AF:

0.175

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Amyloidosis, primary localized cutaneous, 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

May 18, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

IL31RA-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Nov 19, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

5.6

DANN

Benign

0.67

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over