Genetic Variant IL1R1:c.722-136G>T (chr2-102171665-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.722-136G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 408,600 control chromosomes in the GnomAD database, including 22,579 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 0.32 ( 7805 hom., cov: 32)

Exomes 𝑓: 0.32 ( 14774 hom. )

Consequence

IL1R1
NM_000877.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.29

Publications

17 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=-0.75).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4 link	c.722-136G>T		intron_variant	Intron 7 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.722-136G>T		intron_variant	Intron 7 of 11	1	NM_000877.4	ENSP00000386380.1		P14778

Frequencies

GnomAD3 genomes

AF:

0.315

AC:

47861

AN:

151820

Hom.:

7787

Cov.:

show subpopulations

Gnomad AFR

AF:

0.302

Gnomad AMI

AF:

0.303

Gnomad AMR

AF:

0.397

Gnomad ASJ

AF:

0.355

Gnomad EAS

AF:

0.479

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.351

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.285

Gnomad OTH

AF:

0.307

GnomAD4 exome

AF:

0.322

AC:

82771

AN:

256662

Hom.:

14774

AF XY:

0.323

AC XY:

43187

AN XY:

133858

show subpopulations

African (AFR)

AF:

0.301

AC:

2136

AN:

7096

American (AMR)

AF:

0.448

AC:

3618

AN:

8070

Ashkenazi Jewish (ASJ)

AF:

0.360

AC:

3205

AN:

8910

East Asian (EAS)

AF:

0.578

AC:

12484

AN:

21600

South Asian (SAS)

AF:

0.308

AC:

4208

AN:

13680

European-Finnish (FIN)

AF:

0.355

AC:

6978

AN:

19636

Middle Eastern (MID)

AF:

0.217

AC:

273

AN:

1256

European-Non Finnish (NFE)

AF:

0.280

AC:

45037

AN:

160760

Other (OTH)

AF:

0.309

AC:

4832

AN:

15654

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

2515

5031

7546

10062

12577

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

320

640

960

1280

1600

<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:

0.315

AC:

47917

AN:

151938

Hom.:

7805

Cov.:

AF XY:

0.319

AC XY:

23677

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.302

AC:

12518

AN:

41436

American (AMR)

AF:

0.397

AC:

6069

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.355

AC:

1231

AN:

3464

East Asian (EAS)

AF:

0.479

AC:

2469

AN:

5158

South Asian (SAS)

AF:

0.329

AC:

1585

AN:

4820

European-Finnish (FIN)

AF:

0.351

AC:

3696

AN:

10540

Middle Eastern (MID)

AF:

0.252

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.285

AC:

19355

AN:

67936

Other (OTH)

AF:

0.305

AC:

644

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1711

3422

5134

6845

8556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

468

936

1404

1872

2340

<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:

0.295

Hom.:

27627

Bravo

AF:

0.320

Asia WGS

AF:

0.392

AC:

1361

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

1.5

(source)

DANN

Benign

0.83

PhyloP100

-2.3

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