Variant chr2-102386805-C-A 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.810-56C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,564,272 control chromosomes in the GnomAD database, including 33,892 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.17 ( 2482 hom., cov: 32)

Exomes 𝑓: 0.21 ( 31410 hom. )

Consequence

IL18R1
NM_003855.5 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.272

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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.810-56C>A		intron_variant		ENST00000233957.7	NP_003846.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
IL18R1	ENST00000233957.7 linkuse as main transcript	c.810-56C>A	intron_variant	5	NM_003855.5	ENSP00000233957	P1
IL18R1	ENST00000409599.5 linkuse as main transcript	c.810-56C>A	intron_variant	5		ENSP00000387211	P1
IL18R1	ENST00000410040.5 linkuse as main transcript	c.810-56C>A	intron_variant	2		ENSP00000386663
IL18R1	ENST00000677287.1 linkuse as main transcript	c.*354-56C>A	intron_variant, NMD_transcript_variant			ENSP00000503023

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25186

AN:

152044

Hom.:

2481

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0686

Gnomad AMI

AF:

0.171

Gnomad AMR

AF:

0.144

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.229

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.188

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.171

GnomAD4 exome

AF:

0.208

AC:

294129

AN:

1412108

Hom.:

31410

AF XY:

0.210

AC XY:

147845

AN XY:

704844

show subpopulations

Gnomad4 AFR exome

AF:

0.0612

Gnomad4 AMR exome

AF:

0.137

Gnomad4 ASJ exome

AF:

0.126

Gnomad4 EAS exome

AF:

0.201

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.221

Gnomad4 NFE exome

AF:

0.216

Gnomad4 OTH exome

AF:

0.197

GnomAD4 genome

AF:

0.166

AC:

25191

AN:

152164

Hom.:

2482

Cov.:

AF XY:

0.166

AC XY:

12349

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0684

Gnomad4 AMR

AF:

0.144

Gnomad4 ASJ

AF:

0.130

Gnomad4 EAS

AF:

0.229

Gnomad4 SAS

AF:

0.225

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.196

Hom.:

5150

Bravo

AF:

0.156

Asia WGS

AF:

0.245

AC:

854

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Ascending aortic dissection

Other:1

association, no assertion criteria provided

case-control

Beijing Anzhen Hospital, Capital Medical University

Feb 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.3

DANN

Benign

0.40

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over