NM_139017.7:c.155-3517A>G

Variant names:

• chr5-55865274-A-G
• rs10055201
• NM_139017.7:c.155-3517A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_139017.7(IL31RA):​c.155-3517A>G 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 152,102 control chromosomes in the GnomAD database, including 43,936 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 (43936 hom., cov: 32)
• Consequence: IL31RA NM_139017.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 13 publications found

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 Gene-Disease associations (from GenCC):

• familial primary localized cutaneous amyloidosis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• amyloidosis, primary localized cutaneous, 2

  Inheritance: Unknown, AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139017.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL31RA	NM_139017.7	MANE Select	c.155-3517A>G		intron	N/A	NP_620586.3
	IL31RA	NM_001242636.2		c.98-3517A>G		intron	N/A	NP_001229565.1
	IL31RA	NM_001242637.2		c.155-3517A>G		intron	N/A	NP_001229566.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL31RA	ENST00000652347.2	MANE Select	c.155-3517A>G		intron	N/A	ENSP00000498630.1
	IL31RA	ENST00000359040.10	TSL:1	c.155-3517A>G		intron	N/A	ENSP00000351935.5
	IL31RA	ENST00000490985.5	TSL:1	c.-416-1337A>G		intron	N/A	ENSP00000427533.1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114642 AN: 151984 Hom.: 43900 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.786

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.754 AC: 114741 AN: 152102 Hom.: 43936 Cov.: 32 AF XY: 0.752 AC XY: 55892 AN XY: 74326

African (AFR) AF: 0.830 AC: 34458 AN: 41506

American (AMR) AF: 0.591 AC: 9029 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2671 AN: 3466

East Asian (EAS) AF: 0.476 AC: 2462 AN: 5174

South Asian (SAS) AF: 0.769 AC: 3695 AN: 4806

European-Finnish (FIN) AF: 0.786 AC: 8301 AN: 10562

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.759 AC: 51639 AN: 68002

Other (OTH) AF: 0.750 AC: 1579 AN: 2106

Alfa AF: 0.747 Hom.: 71506

Bravo AF: 0.736

Asia WGS AF: 0.661 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.0070
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10055201; hg19: chr5-55161102; COSMIC: COSV51680513;