dbSNP rs2110726: IL1R1:c.*1063G>A (chr2-102177822-G-A) – 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.*1063G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,146 control chromosomes in the GnomAD database, including 7,295 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 0.28 ( 7276 hom., cov: 32)

Exomes 𝑓: 0.39 ( 19 hom. )

Consequence

IL1R1
NM_000877.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.02

Publications

38 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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 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.*1063G>A	3_prime_UTR	Exon 12 of 12	NP_000868.1	P14778
IL1R1	NM_001320978.2		c.*1063G>A	3_prime_UTR	Exon 12 of 12	NP_001307907.1	P14778
IL1R1	NM_001320980.2		c.*1063G>A	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.*1063G>A	3_prime_UTR	Exon 12 of 12	ENSP00000386380.1	P14778
IL1R1	ENST00000853658.1		c.*1063G>A	3_prime_UTR	Exon 12 of 12	ENSP00000523717.1
IL1R1	ENST00000853659.1		c.*1063G>A	3_prime_UTR	Exon 12 of 12	ENSP00000523718.1

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42866

AN:

151780

Hom.:

7273

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0853

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.294

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.353

Gnomad FIN

AF:

0.387

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.293

GnomAD4 exome

AF:

0.391

AC:

AN:

248

Hom.:

Cov.:

AF XY:

0.416

AC XY:

AN XY:

154

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.377

AC:

AN:

138

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.350

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.405

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

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:

0.282

AC:

42865

AN:

151898

Hom.:

7276

Cov.:

AF XY:

0.284

AC XY:

21081

AN XY:

74202

show subpopulations

African (AFR)

AF:

0.0850

AC:

3525

AN:

41450

American (AMR)

AF:

0.256

AC:

3910

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.294

AC:

1017

AN:

3464

East Asian (EAS)

AF:

0.380

AC:

1949

AN:

5128

South Asian (SAS)

AF:

0.353

AC:

1698

AN:

4806

European-Finnish (FIN)

AF:

0.387

AC:

4075

AN:

10540

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.377

AC:

25599

AN:

67940

Other (OTH)

AF:

0.298

AC:

627

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1475

2950

4425

5900

7375

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

452

904

1356

1808

2260

<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:

0.338

Hom.:

15667

Bravo

AF:

0.262

Asia WGS

AF:

0.363

AC:

1260

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.28

(source)

DANN

Benign

0.54

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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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