rs2161582

chr5-55862385-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139017.7(IL31RA):c.154+2786A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,102 control chromosomes in the GnomAD database, including 27,964 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27964 hom., cov: 32)
• Consequence: IL31RA NM_139017.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL31RA	NM_139017.7	c.154+2786A>G		intron_variant		ENST00000652347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL31RA	ENST00000652347.2	c.154+2786A>G		intron_variant			NM_139017.7	A2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90232 AN: 151984 Hom.: 27962 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.603

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.593 AC: 90251 AN: 152102 Hom.: 27964 Cov.: 32 AF XY: 0.594 AC XY: 44183 AN XY: 74356

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.607

Alfa AF: 0.645 Hom.: 4048

Bravo AF: 0.561

Asia WGS AF: 0.567 AC: 1971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	2.2
Dann	Benign	0.72

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

Other links and lift over

dbSNP: rs2161582; hg19: chr5-55158213; COSMIC: COSV51680464;