Variant chr5-55859574-C-T 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.129C>T(p.Pro43=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 1,612,148 control chromosomes in the GnomAD database, including 418,680 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 37265 hom., cov: 32)

Exomes 𝑓: 0.72 ( 381415 hom. )

Consequence

IL31RA
NM_139017.7 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.288

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=-0.88).

BP6

Variant 5-55859574-C-T is Benign according to our data. Variant chr5-55859574-C-T is described in ClinVar as [Benign]. Clinvar id is 1300053.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-55859574-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-0.288 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.744 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.129C>T	p.Pro43=	synonymous_variant	2/15	ENST00000652347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL31RA	ENST00000652347.2 linkuse as main transcript	c.129C>T	p.Pro43=	synonymous_variant	2/15		NM_139017.7	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.696

AC:

105685

AN:

151948

Hom.:

37245

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.722

Gnomad AMR

AF:

0.557

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.782

Gnomad MID

AF:

0.778

Gnomad NFE

AF:

0.737

Gnomad OTH

AF:

0.694

GnomAD3 exomes

AF:

0.676

AC:

170006

AN:

251414

Hom.:

59806

AF XY:

0.692

AC XY:

94083

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.660

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.738

Gnomad EAS exome

AF:

0.465

Gnomad SAS exome

AF:

0.782

Gnomad FIN exome

AF:

0.769

Gnomad NFE exome

AF:

0.736

Gnomad OTH exome

AF:

0.703

GnomAD4 exome

AF:

0.719

AC:

1049850

AN:

1460080

Hom.:

381415

Cov.:

AF XY:

0.723

AC XY:

524905

AN XY:

726504

show subpopulations

Gnomad4 AFR exome

AF:

0.665

Gnomad4 AMR exome

AF:

0.439

Gnomad4 ASJ exome

AF:

0.745

Gnomad4 EAS exome

AF:

0.495

Gnomad4 SAS exome

AF:

0.781

Gnomad4 FIN exome

AF:

0.768

Gnomad4 NFE exome

AF:

0.732

Gnomad4 OTH exome

AF:

0.718

GnomAD4 genome

AF:

0.695

AC:

105761

AN:

152068

Hom.:

37265

Cov.:

AF XY:

0.696

AC XY:

51752

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.671

Gnomad4 AMR

AF:

0.557

Gnomad4 ASJ

AF:

0.736

Gnomad4 EAS

AF:

0.475

Gnomad4 SAS

AF:

0.765

Gnomad4 FIN

AF:

0.782

Gnomad4 NFE

AF:

0.737

Gnomad4 OTH

AF:

0.697

Alfa

AF:

0.714

Hom.:

50433

Bravo

AF:

0.668

Asia WGS

AF:

0.646

AC:

2249

AN:

3478

EpiCase

AF:

0.739

EpiControl

AF:

0.737

ClinVar

Significance: Benign

Submissions summary: Benign:2

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

Aug 19, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.85

DANN

Benign

0.48

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