Variant 5-55883224-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_139017.7(IL31RA):c.606+29A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 1,562,168 control chromosomes in the GnomAD database, including 267,863 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.63 ( 31924 hom., cov: 32)

Exomes 𝑓: 0.57 ( 235939 hom. )

Consequence

IL31RA
NM_139017.7 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0240

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 5-55883224-A-T is Benign according to our data. Variant chr5-55883224-A-T is described in ClinVar as [Benign]. Clinvar id is 1300054.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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.606+29A>T		intron_variant		ENST00000652347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL31RA	ENST00000652347.2 linkuse as main transcript	c.606+29A>T		intron_variant			NM_139017.7	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.633

AC:

95929

AN:

151656

Hom.:

31879

Cov.:

show subpopulations

Gnomad AFR

AF:

0.845

Gnomad AMI

AF:

0.603

Gnomad AMR

AF:

0.458

Gnomad ASJ

AF:

0.584

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.606

Gnomad NFE

AF:

0.577

Gnomad OTH

AF:

0.620

GnomAD3 exomes

AF:

0.551

AC:

137985

AN:

250244

Hom.:

40322

AF XY:

0.558

AC XY:

75530

AN XY:

135344

show subpopulations

Gnomad AFR exome

AF:

0.848

Gnomad AMR exome

AF:

0.339

Gnomad ASJ exome

AF:

0.564

Gnomad EAS exome

AF:

0.375

Gnomad SAS exome

AF:

0.646

Gnomad FIN exome

AF:

0.554

Gnomad NFE exome

AF:

0.576

Gnomad OTH exome

AF:

0.551

GnomAD4 exome

AF:

0.574

AC:

809025

AN:

1410394

Hom.:

235939

Cov.:

AF XY:

0.576

AC XY:

406227

AN XY:

704874

show subpopulations

Gnomad4 AFR exome

AF:

0.852

Gnomad4 AMR exome

AF:

0.355

Gnomad4 ASJ exome

AF:

0.574

Gnomad4 EAS exome

AF:

0.426

Gnomad4 SAS exome

AF:

0.643

Gnomad4 FIN exome

AF:

0.557

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.583

GnomAD4 genome

AF:

0.633

AC:

96037

AN:

151774

Hom.:

31924

Cov.:

AF XY:

0.627

AC XY:

46521

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.845

Gnomad4 AMR

AF:

0.459

Gnomad4 ASJ

AF:

0.584

Gnomad4 EAS

AF:

0.388

Gnomad4 SAS

AF:

0.623

Gnomad4 FIN

AF:

0.553

Gnomad4 NFE

AF:

0.577

Gnomad4 OTH

AF:

0.621

Alfa

AF:

0.607

Hom.:

5265

Bravo

AF:

0.628

Asia WGS

AF:

0.539

AC:

1874

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.3

DANN

Benign

0.43

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