chr2-102384942-C-T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003855.5(IL18R1):​c.753C>T​(p.Phe251=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 1,600,312 control chromosomes in the GnomAD database, including 62,186 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 0.24 ( 4770 hom., cov: 32)
Exomes 𝑓: 0.28 ( 57416 hom. )

Consequence

IL18R1
NM_003855.5 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.326
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=0.326 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL18R1NM_003855.5 linkuse as main transcriptc.753C>T p.Phe251= synonymous_variant 7/11 ENST00000233957.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL18R1ENST00000233957.7 linkuse as main transcriptc.753C>T p.Phe251= synonymous_variant 7/115 NM_003855.5 P1
IL18R1ENST00000409599.5 linkuse as main transcriptc.753C>T p.Phe251= synonymous_variant 8/125 P1
IL18R1ENST00000410040.5 linkuse as main transcriptc.753C>T p.Phe251= synonymous_variant 7/112
IL18R1ENST00000677287.1 linkuse as main transcriptc.*297C>T 3_prime_UTR_variant, NMD_transcript_variant 7/11

Frequencies

GnomAD3 genomes
AF:
0.239
AC:
36149
AN:
151490
Hom.:
4772
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.158
Gnomad AMI
AF:
0.206
Gnomad AMR
AF:
0.191
Gnomad ASJ
AF:
0.153
Gnomad EAS
AF:
0.406
Gnomad SAS
AF:
0.281
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.220
Gnomad NFE
AF:
0.282
Gnomad OTH
AF:
0.231
GnomAD3 exomes
AF:
0.258
AC:
64465
AN:
250070
Hom.:
8983
AF XY:
0.263
AC XY:
35551
AN XY:
135222
show subpopulations
Gnomad AFR exome
AF:
0.152
Gnomad AMR exome
AF:
0.170
Gnomad ASJ exome
AF:
0.154
Gnomad EAS exome
AF:
0.403
Gnomad SAS exome
AF:
0.285
Gnomad FIN exome
AF:
0.273
Gnomad NFE exome
AF:
0.276
Gnomad OTH exome
AF:
0.234
GnomAD4 exome
AF:
0.277
AC:
401598
AN:
1448702
Hom.:
57416
Cov.:
30
AF XY:
0.278
AC XY:
200496
AN XY:
721252
show subpopulations
Gnomad4 AFR exome
AF:
0.147
Gnomad4 AMR exome
AF:
0.172
Gnomad4 ASJ exome
AF:
0.155
Gnomad4 EAS exome
AF:
0.388
Gnomad4 SAS exome
AF:
0.282
Gnomad4 FIN exome
AF:
0.276
Gnomad4 NFE exome
AF:
0.285
Gnomad4 OTH exome
AF:
0.263
GnomAD4 genome
AF:
0.238
AC:
36158
AN:
151610
Hom.:
4770
Cov.:
32
AF XY:
0.238
AC XY:
17652
AN XY:
74066
show subpopulations
Gnomad4 AFR
AF:
0.158
Gnomad4 AMR
AF:
0.190
Gnomad4 ASJ
AF:
0.153
Gnomad4 EAS
AF:
0.406
Gnomad4 SAS
AF:
0.281
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.282
Gnomad4 OTH
AF:
0.238
Alfa
AF:
0.264
Hom.:
8061
Bravo
AF:
0.227
Asia WGS
AF:
0.349
AC:
1213
AN:
3476
EpiCase
AF:
0.269
EpiControl
AF:
0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
5.6
DANN
Benign
0.50

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: rs1035130; hg19: chr2-103001402; COSMIC: COSV52122702; API