dbSNP rs1420106: IL18RAP:c.-694A>G (chr2-102418584-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003853.4(IL18RAP):c.-694A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 152,102 control chromosomes in the GnomAD database, including 46,600 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 0.77 ( 46599 hom., cov: 32)

Exomes 𝑓: 0.75 ( 1 hom. )

Consequence

IL18RAP
NM_003853.4 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Variant links:

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]

IL18RAP links:

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ACMG classification

Classification made for transcript

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 = 0.887 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
IL18RAP	NM_001393486.1 link	c.-554A>G	upstream_gene_variant	NP_001380415.1
IL18RAP	NM_003853.4 link	c.-694A>G	upstream_gene_variant	NP_003844.1	O95256-1
IL18RAP	NM_001393488.1 link	c.-1324A>G	upstream_gene_variant	NP_001380417.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL18RAP	ENST00000264260.6 link	c.-694A>G		upstream_gene_variant		1		ENSP00000264260.2		O95256-1

Frequencies

GnomAD3 genomes

AF:

0.774

AC:

117664

AN:

151980

Hom.:

46551

Cov.:

show subpopulations

Gnomad AFR

AF:

0.894

Gnomad AMI

AF:

0.676

Gnomad AMR

AF:

0.605

Gnomad ASJ

AF:

0.767

Gnomad EAS

AF:

0.551

Gnomad SAS

AF:

0.549

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.756

Gnomad NFE

AF:

0.768

Gnomad OTH

AF:

0.759

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

AF XY:

0.750

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.774

AC:

117763

AN:

152098

Hom.:

46599

Cov.:

AF XY:

0.768

AC XY:

57087

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.894

Gnomad4 AMR

AF:

0.604

Gnomad4 ASJ

AF:

0.767

Gnomad4 EAS

AF:

0.552

Gnomad4 SAS

AF:

0.549

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.768

Gnomad4 OTH

AF:

0.761

Alfa

AF:

0.755

Hom.:

42704

Bravo

AF:

0.764

Asia WGS

AF:

0.583

AC:

2030

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

DANN

Benign

0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over