rs9292101

Positions:

• chr5-55854376-G-T

Variant summary

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

The NM_139017.7(IL31RA):​c.63+2743G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,178 control chromosomes in the GnomAD database, including 43,909 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 0.75 (43909 hom., cov: 33)
• Consequence: IL31RA NM_139017.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL31RA	NM_139017.7	c.63+2743G>T		intron_variant		ENST00000652347.2	NP_620586.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL31RA	ENST00000652347.2	c.63+2743G>T		intron_variant			NM_139017.7	ENSP00000498630	A2

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114629 AN: 152060 Hom.: 43873 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.754 AC: 114728 AN: 152178 Hom.: 43909 Cov.: 33 AF XY: 0.752 AC XY: 55955 AN XY: 74390

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.799

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.746

Alfa AF: 0.770 Hom.: 5648

Bravo AF: 0.734

Asia WGS AF: 0.660 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
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

Other links and lift over

dbSNP: rs9292101; hg19: chr5-55150204; COSMIC: COSV51680409;