rs2058660

chr2-102437989-G-A

Variant summary

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

The NM_001393487.1(IL18RAP):c.730+627G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.776 in 152,188 control chromosomes in the GnomAD database, including 46,913 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 0.78 (46913 hom., cov: 33)
• Consequence: IL18RAP NM_001393487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

IL18RAP (HGNC:5989): (interleukin 18 receptor accessory protein) The protein encoded by this gene is an accessory subunit of the heterodimeric receptor for interleukin 18 (IL18), a proinflammatory cytokine involved in inducing cell-mediated immunity. This protein enhances the IL18-binding activity of the IL18 receptor and plays a role in signaling by IL18. Mutations in this gene are associated with Crohn's disease and inflammatory bowel disease, and susceptibility to celiac disease and leprosy. Alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL18RAP	NM_001393487.1	c.730+627G>A		intron_variant		ENST00000687160.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL18RAP	ENST00000687160.1	c.730+627G>A		intron_variant			NM_001393487.1	P1
IL18RAP	ENST00000264260.6	c.730+627G>A		intron_variant		1		P1
IL18RAP	ENST00000409369.1	c.304+627G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118075 AN: 152066 Hom.: 46870 Cov.: 33

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.776 AC: 118167 AN: 152188 Hom.: 46913 Cov.: 33 AF XY: 0.771 AC XY: 57332 AN XY: 74396

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.758

Alfa AF: 0.753 Hom.: 54167

Bravo AF: 0.766

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.21

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: rs2058660; hg19: chr2-103054449; COSMIC: COSV51824875; COSMIC: COSV51824875;