rs161704

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_139017.7(IL31RA):c.1586G>A(p.Ser529Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,613,250 control chromosomes in the GnomAD database, including 75,081 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.30 ( 7183 hom., cov: 32)

Exomes 𝑓: 0.30 ( 67898 hom. )

Consequence

IL31RA
NM_139017.7 missense

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.327

Publications

26 publications found

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 Gene-Disease associations (from GenCC):

familial primary localized cutaneous amyloidosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
amyloidosis, primary localized cutaneous, 2
Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

IL31RA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0013931394).

BP6

Variant 5-55910616-G-A is Benign according to our data. Variant chr5-55910616-G-A is described in ClinVar as [Benign]. Clinvar id is 3060128.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL31RA	NM_139017.7 link	c.1586G>A	p.Ser529Asn	missense_variant	Exon 12 of 15	ENST00000652347.2	NP_620586.3	Q8NI17-2B4DNJ2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL31RA	ENST00000652347.2 link	c.1586G>A	p.Ser529Asn	missense_variant	Exon 12 of 15		NM_139017.7	ENSP00000498630.1		Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.303

AC:

46112

AN:

151972

Hom.:

7185

Cov.:

show subpopulations

Gnomad AFR

AF:

0.343

Gnomad AMI

AF:

0.508

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.335

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.278

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.281

GnomAD2 exomes

AF:

0.293

AC:

73677

AN:

251458

AF XY:

0.297

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.191

Gnomad ASJ exome

AF:

0.217

Gnomad EAS exome

AF:

0.327

Gnomad FIN exome

AF:

0.282

Gnomad NFE exome

AF:

0.303

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.302

AC:

441483

AN:

1461160

Hom.:

67898

Cov.:

AF XY:

0.304

AC XY:

220815

AN XY:

726980

show subpopulations

African (AFR)

AF:

0.341

AC:

11408

AN:

33470

American (AMR)

AF:

0.198

AC:

8874

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.215

AC:

5618

AN:

26130

East Asian (EAS)

AF:

0.374

AC:

14853

AN:

39696

South Asian (SAS)

AF:

0.362

AC:

31207

AN:

86242

European-Finnish (FIN)

AF:

0.287

AC:

15356

AN:

53414

Middle Eastern (MID)

AF:

0.223

AC:

1288

AN:

5768

European-Non Finnish (NFE)

AF:

0.302

AC:

335510

AN:

1111362

Other (OTH)

AF:

0.288

AC:

17369

AN:

60360

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

16170

32340

48509

64679

80849

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.303

AC:

46137

AN:

152090

Hom.:

7183

Cov.:

AF XY:

0.300

AC XY:

22322

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.342

AC:

14175

AN:

41456

American (AMR)

AF:

0.229

AC:

3499

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

724

AN:

3470

East Asian (EAS)

AF:

0.335

AC:

1734

AN:

5174

South Asian (SAS)

AF:

0.345

AC:

1667

AN:

4826

European-Finnish (FIN)

AF:

0.278

AC:

2941

AN:

10582

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.298

AC:

20274

AN:

67984

Other (OTH)

AF:

0.286

AC:

603

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1613

3227

4840

6454

8067

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.298

Hom.:

26960

Bravo

AF:

0.299

TwinsUK

AF:

0.316

AC:

1170

ALSPAC

AF:

0.309

AC:

1190

ESP6500AA

AF:

0.343

AC:

1511

ESP6500EA

AF:

0.291

AC:

2503

ExAC

AF:

0.301

AC:

36588

Asia WGS

AF:

0.345

AC:

1200

AN:

3478

EpiCase

AF:

0.286

EpiControl

AF:

0.289

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

IL31RA-related disorder

Benign:1

Oct 22, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

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

-0.64

BayesDel_noAF

Benign

-0.55

CADD

Benign

(source)

DANN

Benign

0.25

Eigen

Benign

-0.14

Eigen_PC

Benign

-0.034

FATHMM_MKL

Benign

0.51

LIST_S2

Benign

0.62

.;T;T;T;T;T

MetaRNN

Benign

0.0014

T;T;T;T;T;T

MetaSVM

Benign

-0.99

PhyloP100

0.33

PrimateAI

Benign

0.33

PROVEAN

Benign

-0.10

N;N;N;N;.;N

REVEL

Benign

0.10

Sift

Benign

1.0

T;T;T;T;.;T

Sift4G

Benign

0.24

T;T;T;T;T;T

Polyphen

0.14

B;B;B;B;.;.

Vest4

0.050

MPC

0.11

ClinPred

0.0049

GERP RS

3.3

Mutation Taster

=94/6

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs161704

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over