Genetic Variant IL1R1:c.*1322C>T (chr2-102178081-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000877.4(IL1R1):c.*1322C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0505 in 152,962 control chromosomes in the GnomAD database, including 236 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 0.051 ( 236 hom., cov: 32)

Exomes 𝑓: 0.035 ( 0 hom. )

Consequence

IL1R1
NM_000877.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.543

Publications

19 publications found

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 links:

IL1R1-AS1 (HGNC:53898): (IL1R1 antisense RNA 1)

IL1R1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000877.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL1R1	NM_000877.4	MANE Select	c.*1322C>T	3_prime_UTR	Exon 12 of 12	NP_000868.1	P14778
IL1R1	NM_001320978.2		c.*1322C>T	3_prime_UTR	Exon 12 of 12	NP_001307907.1	P14778
IL1R1	NM_001320980.2		c.*1322C>T	3_prime_UTR	Exon 12 of 12	NP_001307909.1	P14778

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL1R1	ENST00000410023.6	TSL:1 MANE Select	c.*1322C>T	3_prime_UTR	Exon 12 of 12	ENSP00000386380.1	P14778
IL1R1	ENST00000853658.1		c.*1322C>T	3_prime_UTR	Exon 12 of 12	ENSP00000523717.1
IL1R1	ENST00000853659.1		c.*1322C>T	3_prime_UTR	Exon 12 of 12	ENSP00000523718.1

Frequencies

GnomAD3 genomes

AF:

0.0505

AC:

7689

AN:

152196

Hom.:

237

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0648

Gnomad AMI

AF:

0.167

Gnomad AMR

AF:

0.0589

Gnomad ASJ

AF:

0.0657

Gnomad EAS

AF:

0.000769

Gnomad SAS

AF:

0.0118

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.0483

Gnomad OTH

AF:

0.0656

GnomAD4 exome

AF:

0.0355

AC:

AN:

648

Hom.:

Cov.:

AF XY:

0.0389

AC XY:

AN XY:

386

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.0493

AC:

AN:

142

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0216

AC:

AN:

232

Middle Eastern (MID)

AF:

0.0833

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0413

AC:

AN:

218

Other (OTH)

AF:

0.0455

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0505

AC:

7695

AN:

152314

Hom.:

236

Cov.:

AF XY:

0.0491

AC XY:

3659

AN XY:

74490

show subpopulations

African (AFR)

AF:

0.0647

AC:

2691

AN:

41560

American (AMR)

AF:

0.0588

AC:

900

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0657

AC:

228

AN:

3470

East Asian (EAS)

AF:

0.000771

AC:

AN:

5188

South Asian (SAS)

AF:

0.0116

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0185

AC:

197

AN:

10626

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0483

AC:

3287

AN:

68020

Other (OTH)

AF:

0.0649

AC:

137

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

363

726

1088

1451

1814

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0526

Hom.:

328

Bravo

AF:

0.0564

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.99

(source)

DANN

Benign

0.69

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over