chr2-102452327-G-A

Position:

• chr2-102452327-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.*146G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 735,698 control chromosomes in the GnomAD database, including 208,018 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 (46910 hom., cov: 32)
  • Exomes 𝑓: 0.74 (161108 hom.)
• Consequence: IL18RAP NM_001393487.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL18RAP	NM_001393487.1	c.*146G>A		3_prime_UTR_variant	10/10	ENST00000687160.1	NP_001380416.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IL18RAP	ENST00000687160.1	c.*146G>A		3_prime_UTR_variant	10/10		NM_001393487.1	ENSP00000510345	P1
IL18RAP	ENST00000264260.6	c.*146G>A		3_prime_UTR_variant	12/12	1		ENSP00000264260	P1
IL18RAP	ENST00000409369.1	c.*146G>A		3_prime_UTR_variant	10/10	1		ENSP00000387201

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118061 AN: 152056 Hom.: 46867 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.754

GnomAD4 exome AF: 0.737 AC: 430165 AN: 583522 Hom.: 161108 Cov.: 8 AF XY: 0.728 AC XY: 218954 AN XY: 300646

Gnomad4 AFR exome AF: 0.904

Gnomad4 AMR exome AF: 0.525

Gnomad4 ASJ exome AF: 0.769

Gnomad4 EAS exome AF: 0.556

Gnomad4 SAS exome AF: 0.558

Gnomad4 FIN exome AF: 0.813

Gnomad4 NFE exome AF: 0.767

Gnomad4 OTH exome AF: 0.744

GnomAD4 genome AF: 0.776 AC: 118153 AN: 152176 Hom.: 46910 Cov.: 32 AF XY: 0.771 AC XY: 57323 AN XY: 74392

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.810

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.757

Alfa AF: 0.756 Hom.: 44991

Bravo AF: 0.766

Asia WGS AF: 0.579 AC: 2015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.39

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: rs7559479; hg19: chr2-103068787; COSMIC: COSV51830088;