dbSNP rs3917318: IL1R1:c.1304-53A>G (chr2-102176300-A-G) – 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.1304-53A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,519,602 control chromosomes in the GnomAD database, including 73,719 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 0.31 ( 7699 hom., cov: 33)

Exomes 𝑓: 0.30 ( 66020 hom. )

Consequence

IL1R1
NM_000877.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.51

Publications

26 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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4 link	c.1304-53A>G		intron_variant	Intron 11 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.1304-53A>G		intron_variant	Intron 11 of 11	1	NM_000877.4	ENSP00000386380.1		P14778

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47483

AN:

152036

Hom.:

7684

Cov.:

show subpopulations

Gnomad AFR

AF:

0.290

Gnomad AMI

AF:

0.301

Gnomad AMR

AF:

0.394

Gnomad ASJ

AF:

0.354

Gnomad EAS

AF:

0.478

Gnomad SAS

AF:

0.330

Gnomad FIN

AF:

0.354

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.286

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.302

AC:

412696

AN:

1367448

Hom.:

66020

Cov.:

AF XY:

0.302

AC XY:

205172

AN XY:

679252

show subpopulations

African (AFR)

AF:

0.292

AC:

9048

AN:

30984

American (AMR)

AF:

0.527

AC:

20985

AN:

39824

Ashkenazi Jewish (ASJ)

AF:

0.356

AC:

8270

AN:

23212

East Asian (EAS)

AF:

0.545

AC:

21283

AN:

39054

South Asian (SAS)

AF:

0.318

AC:

24424

AN:

76838

European-Finnish (FIN)

AF:

0.355

AC:

17906

AN:

50462

Middle Eastern (MID)

AF:

0.221

AC:

877

AN:

3960

European-Non Finnish (NFE)

AF:

0.280

AC:

292948

AN:

1046462

Other (OTH)

AF:

0.299

AC:

16955

AN:

56652

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

13814

27629

41443

55258

69072

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9946

19892

29838

39784

49730

<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:

0.312

AC:

47534

AN:

152154

Hom.:

7699

Cov.:

AF XY:

0.316

AC XY:

23503

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.290

AC:

12043

AN:

41506

American (AMR)

AF:

0.395

AC:

6038

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.354

AC:

1230

AN:

3470

East Asian (EAS)

AF:

0.478

AC:

2469

AN:

5168

South Asian (SAS)

AF:

0.330

AC:

1589

AN:

4820

European-Finnish (FIN)

AF:

0.354

AC:

3745

AN:

10588

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.286

AC:

19434

AN:

67998

Other (OTH)

AF:

0.303

AC:

639

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1678

3356

5033

6711

8389

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.294

Hom.:

3509

Bravo

AF:

0.317

Asia WGS

AF:

0.392

AC:

1362

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

2.5

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