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GeneBe

2-102175500-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_000877.4(IL1R1):c.1158C>T(p.Asp386=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000785 in 1,613,220 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0026 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00060 ( 5 hom. )

Consequence

IL1R1
NM_000877.4 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.88
Variant links:
Genes affected
IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]
IL1R1-AS1 (HGNC:53898): (IL1R1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 2-102175500-C-T is Benign according to our data. Variant chr2-102175500-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 723970.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=1.88 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 390 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IL1R1NM_000877.4 linkuse as main transcriptc.1158C>T p.Asp386= synonymous_variant 11/12 ENST00000410023.6
IL1R1-AS1NR_174960.1 linkuse as main transcriptn.306-2803G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IL1R1ENST00000410023.6 linkuse as main transcriptc.1158C>T p.Asp386= synonymous_variant 11/121 NM_000877.4 P1
IL1R1-AS1ENST00000428188.1 linkuse as main transcriptn.306-2803G>A intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00256
AC:
390
AN:
152148
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00809
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000589
Gnomad ASJ
AF:
0.000864
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000500
Gnomad OTH
AF:
0.00334
GnomAD3 exomes
AF:
0.000836
AC:
210
AN:
251300
Hom.:
0
AF XY:
0.000677
AC XY:
92
AN XY:
135822
show subpopulations
Gnomad AFR exome
AF:
0.00824
Gnomad AMR exome
AF:
0.000521
Gnomad ASJ exome
AF:
0.000595
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000378
Gnomad OTH exome
AF:
0.00114
GnomAD4 exome
AF:
0.000596
AC:
871
AN:
1460954
Hom.:
5
Cov.:
30
AF XY:
0.000598
AC XY:
435
AN XY:
726848
show subpopulations
Gnomad4 AFR exome
AF:
0.00915
Gnomad4 AMR exome
AF:
0.000559
Gnomad4 ASJ exome
AF:
0.000766
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000580
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000349
Gnomad4 OTH exome
AF:
0.00172
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00260
AC:
396
AN:
152266
Hom.:
2
Cov.:
32
AF XY:
0.00236
AC XY:
176
AN XY:
74434
show subpopulations
Gnomad4 AFR
AF:
0.00823
Gnomad4 AMR
AF:
0.000588
Gnomad4 ASJ
AF:
0.000864
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000485
Gnomad4 OTH
AF:
0.00331
Alfa
AF:
0.00149
Hom.:
0
Bravo
AF:
0.00294
Asia WGS
AF:
0.00260
AC:
9
AN:
3478
EpiCase
AF:
0.000655
EpiControl
AF:
0.000593

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenAug 01, 2022IL1R1: BP4, BP7 -
Benign, criteria provided, single submitterclinical testingInvitaeJul 07, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.40
Cadd
Benign
12
Dann
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs113665542; hg19: chr2-102791960; COSMIC: COSV52107438; COSMIC: COSV52107438; API