2-102381261-C-T

Variant summary

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

The NM_003855.5(IL18R1):​c.626-359C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,774 control chromosomes in the GnomAD database, including 23,437 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 0.53 ( 23437 hom., cov: 32)

Consequence

IL18R1
NM_003855.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL18R1NM_003855.5 linkuse as main transcriptc.626-359C>T intron_variant ENST00000233957.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL18R1ENST00000233957.7 linkuse as main transcriptc.626-359C>T intron_variant 5 NM_003855.5 P1
IL18R1ENST00000409599.5 linkuse as main transcriptc.626-359C>T intron_variant 5 P1
IL18R1ENST00000410040.5 linkuse as main transcriptc.626-359C>T intron_variant 2
IL18R1ENST00000677287.1 linkuse as main transcriptc.*170-359C>T intron_variant, NMD_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
80913
AN:
151656
Hom.:
23405
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.730
Gnomad AMI
AF:
0.466
Gnomad AMR
AF:
0.413
Gnomad ASJ
AF:
0.613
Gnomad EAS
AF:
0.150
Gnomad SAS
AF:
0.265
Gnomad FIN
AF:
0.540
Gnomad MID
AF:
0.523
Gnomad NFE
AF:
0.486
Gnomad OTH
AF:
0.525
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.534
AC:
80998
AN:
151774
Hom.:
23437
Cov.:
32
AF XY:
0.527
AC XY:
39114
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.730
Gnomad4 AMR
AF:
0.412
Gnomad4 ASJ
AF:
0.613
Gnomad4 EAS
AF:
0.150
Gnomad4 SAS
AF:
0.265
Gnomad4 FIN
AF:
0.540
Gnomad4 NFE
AF:
0.486
Gnomad4 OTH
AF:
0.520
Alfa
AF:
0.500
Hom.:
2350
Bravo
AF:
0.535
Asia WGS
AF:
0.232
AC:
807
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.2
DANN
Benign
0.46

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: rs7584093; hg19: chr2-102997721; COSMIC: COSV52123473; API