Genetic Variant IL1R1:c.-83-12285G>A (chr2-102141656-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 ENST00000409929.5(IL1R1):c.-83-12285G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,028 control chromosomes in the GnomAD database, including 14,876 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 0.42 ( 14875 hom., cov: 32)

Exomes 𝑓: 0.29 ( 1 hom. )

Consequence

IL1R1
ENST00000409929.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.133

Publications

24 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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409929.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
IL1R1	NM_001320978.2	c.-83-12285G>A	intron	N/A	NP_001307907.1
IL1R1	NM_001320980.2	c.-83-12285G>A	intron	N/A	NP_001307909.1
IL1R1	NM_001288706.2	c.-83-12285G>A	intron	N/A	NP_001275635.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL1R1	ENST00000409929.5	TSL:1	c.-83-12285G>A	intron	N/A	ENSP00000386776.1
IL1R1	ENST00000409329.5	TSL:5	c.-83-12285G>A	intron	N/A	ENSP00000387131.1
IL1R1	ENST00000424272.5	TSL:5	c.-83-12285G>A	intron	N/A	ENSP00000415366.1

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63008

AN:

151872

Hom.:

14852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.658

Gnomad AMI

AF:

0.420

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.316

Gnomad SAS

AF:

0.385

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.289

AC:

AN:

Hom.:

AF XY:

0.273

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

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:

0.415

AC:

63092

AN:

151990

Hom.:

14875

Cov.:

AF XY:

0.412

AC XY:

30592

AN XY:

74280

show subpopulations

African (AFR)

AF:

0.658

AC:

27256

AN:

41418

American (AMR)

AF:

0.344

AC:

5254

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.420

AC:

1456

AN:

3468

East Asian (EAS)

AF:

0.317

AC:

1635

AN:

5164

South Asian (SAS)

AF:

0.385

AC:

1854

AN:

4820

European-Finnish (FIN)

AF:

0.271

AC:

2862

AN:

10548

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21439

AN:

67982

Other (OTH)

AF:

0.392

AC:

825

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1720

3439

5159

6878

8598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

562

1124

1686

2248

2810

<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.:

5261

Bravo

AF:

0.428

Asia WGS

AF:

0.374

AC:

1303

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.1

(source)

DANN

Benign

0.42

PhyloP100

-0.13

PromoterAI

0.017

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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