rs10204137

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016232.5(IL1RL1):c.1502A>G(p.Gln501Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 1,612,806 control chromosomes in the GnomAD database, including 122,646 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.45 ( 17654 hom., cov: 30)

Exomes 𝑓: 0.37 ( 104992 hom. )

Consequence

IL1RL1
NM_016232.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.111

Publications

51 publications found

Variant links:

Genes affected

IL1RL1 (HGNC:5998): (interleukin 1 receptor like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family. Studies of the similar gene in mouse suggested that this receptor can be induced by proinflammatory stimuli, and may be involved in the function of helper T cells. This gene, interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2) and interleukin 1 receptor-like 2 (IL1RL2) form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008]

IL1RL1 links:

IL18R1 (HGNC:5988): (interleukin 18 receptor 1) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This receptor specifically binds interleukin 18 (IL18), and is essential for IL18 mediated signal transduction. IFN-alpha and IL12 are reported to induce the expression of this receptor in NK and T cells. This gene along with four other members of the interleukin 1 receptor family, including IL1R2, IL1R1, ILRL2 (IL-1Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on chromosome 2q. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

IL18R1 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 (MetaRNN=1.002102E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RL1	NM_016232.5 link	c.1502A>G	p.Gln501Arg	missense_variant	Exon 11 of 11	ENST00000233954.6	NP_057316.3	Q01638-1
IL1RL1	XM_006712839.4 link	c.1502A>G	p.Gln501Arg	missense_variant	Exon 11 of 11		XP_006712902.1	Q01638-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 link	c.1502A>G	p.Gln501Arg	missense_variant	Exon 11 of 11	1	NM_016232.5	ENSP00000233954.1		Q01638-1
IL18R1	ENST00000410040.5 link	c.-28-10881A>G		intron_variant	Intron 1 of 10	2		ENSP00000386663.1		Q13478

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68387

AN:

151676

Hom.:

17625

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

0.402

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.477

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.200

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.414

GnomAD2 exomes

AF:

0.341

AC:

85563

AN:

250992

AF XY:

0.332

show subpopulations

Gnomad AFR exome

AF:

0.710

Gnomad AMR exome

AF:

0.218

Gnomad ASJ exome

AF:

0.462

Gnomad EAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.416

Gnomad NFE exome

AF:

0.379

Gnomad OTH exome

AF:

0.371

GnomAD4 exome

AF:

0.368

AC:

538251

AN:

1461012

Hom.:

104992

Cov.:

AF XY:

0.362

AC XY:

263132

AN XY:

726854

show subpopulations

African (AFR)

AF:

0.714

AC:

23885

AN:

33472

American (AMR)

AF:

0.230

AC:

10267

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.469

AC:

12243

AN:

26132

East Asian (EAS)

AF:

0.151

AC:

5972

AN:

39662

South Asian (SAS)

AF:

0.183

AC:

15818

AN:

86244

European-Finnish (FIN)

AF:

0.414

AC:

22129

AN:

53404

Middle Eastern (MID)

AF:

0.283

AC:

1632

AN:

5766

European-Non Finnish (NFE)

AF:

0.381

AC:

423911

AN:

1111248

Other (OTH)

AF:

0.371

AC:

22394

AN:

60372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.462

Heterozygous variant carriers

17602

35204

52805

70407

88009

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13198

26396

39594

52792

65990

<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:

0.451

AC:

68466

AN:

151794

Hom.:

17654

Cov.:

AF XY:

0.444

AC XY:

32954

AN XY:

74220

show subpopulations

African (AFR)

AF:

0.701

AC:

29002

AN:

41350

American (AMR)

AF:

0.317

AC:

4844

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1653

AN:

3466

East Asian (EAS)

AF:

0.128

AC:

660

AN:

5162

South Asian (SAS)

AF:

0.199

AC:

958

AN:

4814

European-Finnish (FIN)

AF:

0.421

AC:

4431

AN:

10532

Middle Eastern (MID)

AF:

0.250

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.377

AC:

25614

AN:

67892

Other (OTH)

AF:

0.410

AC:

865

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1683

3365

5048

6730

8413

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

588

1176

1764

2352

2940

<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:

0.397

Hom.:

15275

Bravo

AF:

0.457

TwinsUK

AF:

0.377

AC:

1398

ALSPAC

AF:

0.373

AC:

1436

ESP6500AA

AF:

0.0999

AC:

440

ESP6500EA

AF:

0.0276

AC:

237

ExAC

AF:

0.349

AC:

42335

Asia WGS

AF:

0.180

AC:

627

AN:

3478

EpiCase

AF:

0.380

EpiControl

AF:

0.383

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.061

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.10

(source)

DANN

Benign

0.44

DEOGEN2

Benign

0.030

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.026

LIST_S2

Benign

0.24

MetaRNN

Benign

0.0000010

MetaSVM

Benign

-0.99

MutationAssessor

Benign

0.43

PhyloP100

0.11

PrimateAI

Benign

0.22

PROVEAN

Benign

0.99

REVEL

Benign

0.028

Sift

Benign

0.66

Sift4G

Benign

0.73

Polyphen

0.0

Vest4

0.0090

MPC

0.010

ClinPred

0.0046

GERP RS

-0.57

Varity_R

0.026

gMVP

0.15

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