Genetic Variant IL1R1:c.486+147G>T (chr2-102165451-G-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.486+147G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 449,708 control chromosomes in the GnomAD database, including 1,679 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 0.094 ( 846 hom., cov: 32)

Exomes 𝑓: 0.067 ( 833 hom. )

Consequence

IL1R1
NM_000877.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.40

Publications

8 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:

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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4 link	c.486+147G>T		intron_variant	Intron 5 of 11	ENST00000410023.6	NP_000868.1	P14778

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6 link	c.486+147G>T		intron_variant	Intron 5 of 11	1	NM_000877.4	ENSP00000386380.1		P14778

Frequencies

GnomAD3 genomes

AF:

0.0945

AC:

14372

AN:

152054

Hom.:

849

Cov.:

show subpopulations

Gnomad AFR

AF:

0.150

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0749

Gnomad ASJ

AF:

0.0589

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0145

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0765

Gnomad OTH

AF:

0.0852

GnomAD4 exome

AF:

0.0666

AC:

19819

AN:

297536

Hom.:

833

AF XY:

0.0659

AC XY:

10077

AN XY:

152924

show subpopulations

African (AFR)

AF:

0.143

AC:

1096

AN:

7674

American (AMR)

AF:

0.0600

AC:

612

AN:

10204

Ashkenazi Jewish (ASJ)

AF:

0.0517

AC:

497

AN:

9610

East Asian (EAS)

AF:

0.000169

AC:

AN:

23732

South Asian (SAS)

AF:

0.0112

AC:

127

AN:

11298

European-Finnish (FIN)

AF:

0.104

AC:

2856

AN:

27518

Middle Eastern (MID)

AF:

0.0486

AC:

AN:

1338

European-Non Finnish (NFE)

AF:

0.0707

AC:

13303

AN:

188282

Other (OTH)

AF:

0.0704

AC:

1259

AN:

17880

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

824

1648

2473

3297

4121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

118

236

354

472

590

<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:

0.0945

AC:

14376

AN:

152172

Hom.:

846

Cov.:

AF XY:

0.0953

AC XY:

7093

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.150

AC:

6225

AN:

41512

American (AMR)

AF:

0.0748

AC:

1143

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0589

AC:

204

AN:

3466

East Asian (EAS)

AF:

0.000386

AC:

AN:

5188

South Asian (SAS)

AF:

0.0143

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.125

AC:

1320

AN:

10584

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0765

AC:

5199

AN:

67992

Other (OTH)

AF:

0.0843

AC:

178

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

661

1322

1983

2644

3305

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

150

300

450

600

750

<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:

0.0846

Hom.:

675

Bravo

AF:

0.0938

Asia WGS

AF:

0.0170

AC:

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.0090

(source)

DANN

Benign

0.65

PhyloP100

-3.4

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over