chr2-102357669-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003855.5(IL18R1):​c.-29+1269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 151,770 control chromosomes in the GnomAD database, including 8,367 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign,association (★★).

Frequency

Genomes: 𝑓 0.32 ( 8367 hom., cov: 30)

Consequence

IL18R1
NM_003855.5 intron

Scores

2

Clinical Significance

Benign; association criteria provided, multiple submitters, no conflicts B:1O:1

Conservation

PhyloP100: -1.25
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
Variant 2-102357669-C-T is Benign according to our data. Variant chr2-102357669-C-T is described in ClinVar as [Benign, association]. Clinvar id is 916546.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL18R1NM_003855.5 linkc.-29+1269C>T intron_variant ENST00000233957.7 NP_003846.1 Q13478

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL18R1ENST00000233957.7 linkc.-29+1269C>T intron_variant 5 NM_003855.5 ENSP00000233957.1 Q13478
IL18R1ENST00000409599.5 linkc.-29+1269C>T intron_variant 5 ENSP00000387211.1 Q13478
IL18R1ENST00000410040.5 linkc.-28-4964C>T intron_variant 2 ENSP00000386663.1 Q13478
IL18R1ENST00000466357.1 linkn.356+1269C>T intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.316
AC:
47973
AN:
151652
Hom.:
8366
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.170
Gnomad AMI
AF:
0.271
Gnomad AMR
AF:
0.278
Gnomad ASJ
AF:
0.307
Gnomad EAS
AF:
0.427
Gnomad SAS
AF:
0.355
Gnomad FIN
AF:
0.389
Gnomad MID
AF:
0.528
Gnomad NFE
AF:
0.391
Gnomad OTH
AF:
0.347
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.316
AC:
47996
AN:
151770
Hom.:
8367
Cov.:
30
AF XY:
0.317
AC XY:
23503
AN XY:
74154
show subpopulations
Gnomad4 AFR
AF:
0.170
Gnomad4 AMR
AF:
0.278
Gnomad4 ASJ
AF:
0.307
Gnomad4 EAS
AF:
0.427
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.389
Gnomad4 NFE
AF:
0.391
Gnomad4 OTH
AF:
0.353
Alfa
AF:
0.334
Hom.:
1736
Bravo
AF:
0.299
Asia WGS
AF:
0.408
AC:
1418
AN:
3478

ClinVar

Significance: Benign; association
Submissions summary: Benign:1Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 13, 2018This variant is associated with the following publications: (PMID: 28121058) -
Behcet disease Other:1
association, criteria provided, single submittercase-controlChongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical UniversityJan 29, 2020- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
1.1
DANN
Benign
0.52

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.

Other links and lift over

dbSNP: rs12999364; hg19: chr2-102974129; API