Variant chr5-55872304-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_139017.7(IL31RA):c.307A>G(p.Asn103Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,613,286 control chromosomes in the GnomAD database, including 1,192 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.054 ( 474 hom., cov: 32)

Exomes 𝑓: 0.022 ( 718 hom. )

Consequence

IL31RA
NM_139017.7 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.0740

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013972521).

BP6

Variant 5-55872304-A-G is Benign according to our data. Variant chr5-55872304-A-G is described in ClinVar as [Benign]. Clinvar id is 3056087.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL31RA	NM_139017.7 linkuse as main transcript	c.307A>G	p.Asn103Asp	missense_variant	4/15	ENST00000652347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL31RA	ENST00000652347.2 linkuse as main transcript	c.307A>G	p.Asn103Asp	missense_variant	4/15		NM_139017.7	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.0541

AC:

8228

AN:

152122

Hom.:

474

Cov.:

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.00659

Gnomad AMR

AF:

0.0270

Gnomad ASJ

AF:

0.0415

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00415

Gnomad FIN

AF:

0.0170

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0192

Gnomad OTH

AF:

0.0430

GnomAD3 exomes

AF:

0.0246

AC:

6169

AN:

251118

Hom.:

248

AF XY:

0.0213

AC XY:

2891

AN XY:

135734

show subpopulations

Gnomad AFR exome

AF:

0.151

Gnomad AMR exome

AF:

0.0167

Gnomad ASJ exome

AF:

0.0384

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00311

Gnomad FIN exome

AF:

0.0166

Gnomad NFE exome

AF:

0.0192

Gnomad OTH exome

AF:

0.0209

GnomAD4 exome

AF:

0.0221

AC:

32283

AN:

1461046

Hom.:

718

Cov.:

AF XY:

0.0212

AC XY:

15430

AN XY:

726842

show subpopulations

Gnomad4 AFR exome

AF:

0.153

Gnomad4 AMR exome

AF:

0.0185

Gnomad4 ASJ exome

AF:

0.0379

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.00313

Gnomad4 FIN exome

AF:

0.0152

Gnomad4 NFE exome

AF:

0.0201

Gnomad4 OTH exome

AF:

0.0296

GnomAD4 genome

AF:

0.0541

AC:

8238

AN:

152240

Hom.:

474

Cov.:

AF XY:

0.0519

AC XY:

3865

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.146

Gnomad4 AMR

AF:

0.0269

Gnomad4 ASJ

AF:

0.0415

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00374

Gnomad4 FIN

AF:

0.0170

Gnomad4 NFE

AF:

0.0192

Gnomad4 OTH

AF:

0.0430

Alfa

AF:

0.0252

Hom.:

185

Bravo

AF:

0.0606

TwinsUK

AF:

0.0208

AC:

ALSPAC

AF:

0.0171

AC:

ESP6500AA

AF:

0.144

AC:

634

ESP6500EA

AF:

0.0233

AC:

200

ExAC

AF:

0.0266

AC:

3232

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.0185

EpiControl

AF:

0.0170

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

IL31RA-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 26, 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_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.76

CADD

Benign

1.6

DANN

Benign

0.68

DEOGEN2

Benign

0.0023

.;.;.;.;.;.;T

Eigen

Benign

-1.3

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0074

LIST_S2

Benign

0.49

T;.;T;T;T;T;T

MetaRNN

Benign

0.0014

T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

P;P;P;P;P;P;P

PrimateAI

Benign

0.28

PROVEAN

Benign

-0.69

N;N;N;N;N;.;.

REVEL

Benign

0.014

Sift

Benign

0.30

T;T;T;T;T;.;.

Sift4G

Benign

0.34

T;T;T;T;T;T;T

Polyphen

0.0010

B;B;B;B;B;.;.

Vest4

0.045

MPC

0.13

ClinPred

0.0035

GERP RS

-2.5

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over