Variant chr5-55916618-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_139017.7(IL31RA):c.1819-26T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,602,264 control chromosomes in the GnomAD database, including 56,177 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.22 ( 4554 hom., cov: 31)

Exomes 𝑓: 0.26 ( 51623 hom. )

Consequence

IL31RA
NM_139017.7 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.476

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 5-55916618-T-G is Benign according to our data. Variant chr5-55916618-T-G is described in ClinVar as [Benign]. Clinvar id is 1300055.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 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.1819-26T>G		intron_variant		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.1819-26T>G		intron_variant			NM_139017.7	ENSP00000498630	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33444

AN:

151882

Hom.:

4559

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0645

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.325

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.250

Gnomad OTH

AF:

0.224

GnomAD3 exomes

AF:

0.285

AC:

71709

AN:

251254

Hom.:

11342

AF XY:

0.287

AC XY:

38914

AN XY:

135820

show subpopulations

Gnomad AFR exome

AF:

0.0616

Gnomad AMR exome

AF:

0.356

Gnomad ASJ exome

AF:

0.339

Gnomad EAS exome

AF:

0.493

Gnomad SAS exome

AF:

0.302

Gnomad FIN exome

AF:

0.300

Gnomad NFE exome

AF:

0.250

Gnomad OTH exome

AF:

0.291

GnomAD4 exome

AF:

0.260

AC:

377663

AN:

1450264

Hom.:

51623

Cov.:

AF XY:

0.262

AC XY:

189087

AN XY:

722208

show subpopulations

Gnomad4 AFR exome

AF:

0.0571

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.340

Gnomad4 EAS exome

AF:

0.442

Gnomad4 SAS exome

AF:

0.303

Gnomad4 FIN exome

AF:

0.293

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.265

GnomAD4 genome

AF:

0.220

AC:

33445

AN:

152000

Hom.:

4554

Cov.:

AF XY:

0.229

AC XY:

16982

AN XY:

74278

show subpopulations

Gnomad4 AFR

AF:

0.0646

Gnomad4 AMR

AF:

0.306

Gnomad4 ASJ

AF:

0.325

Gnomad4 EAS

AF:

0.477

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.250

Gnomad4 OTH

AF:

0.224

Alfa

AF:

0.248

Hom.:

9175

Bravo

AF:

0.216

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

-0.82

CADD

Benign

5.2

DANN

Benign

0.60

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