dbSNP rs3917289: 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

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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