Variant rs1420098 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_003855.5(IL18R1):c.59-6T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 1,604,718 control chromosomes in the GnomAD database, including 115,560 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9022 hom., cov: 32)

Exomes 𝑓: 0.38 ( 106538 hom. )

Consequence

IL18R1
NM_003855.5 splice_region, intron

Scores

Splicing: ADA: 0.0001448

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.558

Variant links:

Genes affected

IL18R1 (HGNC:5988): (interleukin 18 receptor 1) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This receptor specifically binds interleukin 18 (IL18), and is essential for IL18 mediated signal transduction. IFN-alpha and IL12 are reported to induce the expression of this receptor in NK and T cells. This gene along with four other members of the interleukin 1 receptor family, including IL1R2, IL1R1, ILRL2 (IL-1Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on chromosome 2q. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

IL18R1 links:

IL18R1 (HGNC:):

IL18R1 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL18R1	NM_003855.5 linkuse as main transcript	c.59-6T>C		splice_region_variant, intron_variant		ENST00000233957.7	NP_003846.1	Q13478

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
IL18R1	ENST00000233957.7 linkuse as main transcript	c.59-6T>C	splice_region_variant, intron_variant	5	NM_003855.5	ENSP00000233957.1	Q13478
IL18R1	ENST00000409599.5 linkuse as main transcript	c.59-6T>C	splice_region_variant, intron_variant	5		ENSP00000387211.1	Q13478
IL18R1	ENST00000410040.5 linkuse as main transcript	c.59-6T>C	splice_region_variant, intron_variant	2		ENSP00000386663.1	Q13478
IL18R1	ENST00000677287.1 linkuse as main transcript	n.59-6T>C	splice_region_variant, intron_variant			ENSP00000503023.1	Q86YL8

Frequencies

GnomAD3 genomes

AF:

0.335

AC:

50953

AN:

152004

Hom.:

9021

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.271

Gnomad AMR

AF:

0.290

Gnomad ASJ

AF:

0.307

Gnomad EAS

AF:

0.428

Gnomad SAS

AF:

0.356

Gnomad FIN

AF:

0.388

Gnomad MID

AF:

0.532

Gnomad NFE

AF:

0.391

Gnomad OTH

AF:

0.359

GnomAD3 exomes

AF:

0.355

AC:

86656

AN:

244440

Hom.:

15702

AF XY:

0.363

AC XY:

47887

AN XY:

132050

show subpopulations

Gnomad AFR exome

AF:

0.230

Gnomad AMR exome

AF:

0.233

Gnomad ASJ exome

AF:

0.316

Gnomad EAS exome

AF:

0.429

Gnomad SAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.394

Gnomad NFE exome

AF:

0.387

Gnomad OTH exome

AF:

0.358

GnomAD4 exome

AF:

0.381

AC:

553523

AN:

1452592

Hom.:

106538

Cov.:

AF XY:

0.382

AC XY:

275652

AN XY:

721676

show subpopulations

Gnomad4 AFR exome

AF:

0.230

Gnomad4 AMR exome

AF:

0.241

Gnomad4 ASJ exome

AF:

0.312

Gnomad4 EAS exome

AF:

0.408

Gnomad4 SAS exome

AF:

0.373

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.391

Gnomad4 OTH exome

AF:

0.380

GnomAD4 genome

AF:

0.335

AC:

50981

AN:

152126

Hom.:

9022

Cov.:

AF XY:

0.336

AC XY:

24960

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.234

Gnomad4 AMR

AF:

0.290

Gnomad4 ASJ

AF:

0.307

Gnomad4 EAS

AF:

0.429

Gnomad4 SAS

AF:

0.357

Gnomad4 FIN

AF:

0.388

Gnomad4 NFE

AF:

0.391

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.358

Hom.:

6242

Bravo

AF:

0.321

Asia WGS

AF:

0.411

AC:

1429

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

8.1

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00014

dbscSNV1_RF

Benign

0.016

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

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