dbSNP rs956730: 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:

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=-0.9).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
IL1R1	NM_001320978.2 link	c.-83-12285G>A	intron_variant	Intron 1 of 11	NP_001307907.1	P14778
IL1R1	NM_001320980.2 link	c.-83-12285G>A	intron_variant	Intron 1 of 11	NP_001307909.1	P14778
IL1R1	NM_001288706.2 link	c.-83-12285G>A	intron_variant	Intron 1 of 11	NP_001275635.1	P14778B8ZZW4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
IL1R1	ENST00000409929.5 link	c.-83-12285G>A	intron_variant	Intron 1 of 11	1	ENSP00000386776.1	B8ZZW4
IL1R1	ENST00000409329.5 link	c.-83-12285G>A	intron_variant	Intron 1 of 10	5	ENSP00000387131.1	B8ZZ73
IL1R1	ENST00000424272.5 link	c.-83-12285G>A	intron_variant	Intron 1 of 10	5	ENSP00000415366.1	B8ZZ73

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over