Variant chr2-102396928-TG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_003855.5(IL18R1):c.*46del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 1,242,206 control chromosomes in the GnomAD database, including 714 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.024 ( 49 hom., cov: 32)

Exomes 𝑓: 0.031 ( 665 hom. )

Consequence

IL18R1
NM_003855.5 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.215

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0243 (3706/152304) while in subpopulation NFE AF= 0.0373 (2534/68026). AF 95% confidence interval is 0.036. There are 49 homozygotes in gnomad4. There are 1846 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 49 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IL18R1	NM_003855.5 linkuse as main transcript	c.*46del		3_prime_UTR_variant	11/11	ENST00000233957.7	NP_003846.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
IL18R1	ENST00000233957.7 linkuse as main transcript	c.*46del	3_prime_UTR_variant	11/11	5	NM_003855.5	ENSP00000233957	P1
IL18R1	ENST00000409599.5 linkuse as main transcript	c.*46del	3_prime_UTR_variant	12/12	5		ENSP00000387211	P1
IL18R1	ENST00000677287.1 linkuse as main transcript	c.*1216del	3_prime_UTR_variant, NMD_transcript_variant	11/11			ENSP00000503023
IL18R1	ENST00000410040.5 linkuse as main transcript		downstream_gene_variant		2		ENSP00000386663

Frequencies

GnomAD3 genomes

AF:

0.0244

AC:

3708

AN:

152186

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00680

Gnomad AMI

AF:

0.0143

Gnomad AMR

AF:

0.0139

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0346

Gnomad FIN

AF:

0.0407

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0372

Gnomad OTH

AF:

0.0215

GnomAD3 exomes

AF:

0.0273

AC:

4533

AN:

166066

Hom.:

AF XY:

0.0285

AC XY:

2514

AN XY:

88196

show subpopulations

Gnomad AFR exome

AF:

0.00683

Gnomad AMR exome

AF:

0.0196

Gnomad ASJ exome

AF:

0.00665

Gnomad EAS exome

AF:

0.000475

Gnomad SAS exome

AF:

0.0343

Gnomad FIN exome

AF:

0.0382

Gnomad NFE exome

AF:

0.0348

Gnomad OTH exome

AF:

0.0333

GnomAD4 exome

AF:

0.0314

AC:

34217

AN:

1089902

Hom.:

665

Cov.:

AF XY:

0.0318

AC XY:

17503

AN XY:

549648

show subpopulations

Gnomad4 AFR exome

AF:

0.00505

Gnomad4 AMR exome

AF:

0.0186

Gnomad4 ASJ exome

AF:

0.00483

Gnomad4 EAS exome

AF:

0.000899

Gnomad4 SAS exome

AF:

0.0381

Gnomad4 FIN exome

AF:

0.0375

Gnomad4 NFE exome

AF:

0.0341

Gnomad4 OTH exome

AF:

0.0268

GnomAD4 genome

AF:

0.0243

AC:

3706

AN:

152304

Hom.:

Cov.:

AF XY:

0.0248

AC XY:

1846

AN XY:

74466

show subpopulations

Gnomad4 AFR

AF:

0.00678

Gnomad4 AMR

AF:

0.0139

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0342

Gnomad4 FIN

AF:

0.0407

Gnomad4 NFE

AF:

0.0373

Gnomad4 OTH

AF:

0.0213

Alfa

AF:

0.0293

Hom.:

Bravo

AF:

0.0211

Asia WGS

AF:

0.0170

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

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