rs10206753

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.1652T>C(p.Leu551Ser) 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 1,607,608 control chromosomes in the GnomAD database, including 122,423 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 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 ( 17659 hom., cov: 31)

Exomes 𝑓: 0.37 ( 104764 hom. )

Consequence

IL1RL1
NM_016232.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.346

Publications

59 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=3.3796666E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RL1	NM_016232.5 link	c.1652T>C	p.Leu551Ser	missense_variant	Exon 11 of 11	ENST00000233954.6	NP_057316.3
IL1RL1	XM_006712839.4 link	c.1652T>C	p.Leu551Ser	missense_variant	Exon 11 of 11		XP_006712902.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RL1	ENST00000233954.6 link	c.1652T>C	p.Leu551Ser	missense_variant	Exon 11 of 11	1	NM_016232.5	ENSP00000233954.1
IL18R1	ENST00000410040.5 link	c.-28-10731T>C		intron_variant	Intron 1 of 10	2		ENSP00000386663.1

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68417

AN:

151758

Hom.:

17630

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:

0.201

Gnomad FIN

AF:

0.421

Gnomad MID

AF:

0.242

Gnomad NFE

AF:

0.377

Gnomad OTH

AF:

0.413

GnomAD2 exomes

AF:

0.340

AC:

84245

AN:

247912

AF XY:

0.332

show subpopulations

Gnomad AFR exome

AF:

0.710

Gnomad AMR exome

AF:

0.218

Gnomad ASJ exome

AF:

0.461

Gnomad EAS exome

AF:

0.115

Gnomad FIN exome

AF:

0.416

Gnomad NFE exome

AF:

0.379

Gnomad OTH exome

AF:

0.370

GnomAD4 exome

AF:

0.368

AC:

535882

AN:

1455732

Hom.:

104764

Cov.:

AF XY:

0.362

AC XY:

261983

AN XY:

724322

show subpopulations

African (AFR)

AF:

0.714

AC:

23769

AN:

33284

American (AMR)

AF:

0.230

AC:

10239

AN:

44554

Ashkenazi Jewish (ASJ)

AF:

0.468

AC:

12095

AN:

25854

East Asian (EAS)

AF:

0.150

AC:

5956

AN:

39662

South Asian (SAS)

AF:

0.183

AC:

15748

AN:

85928

European-Finnish (FIN)

AF:

0.414

AC:

22065

AN:

53274

Middle Eastern (MID)

AF:

0.282

AC:

1514

AN:

5360

European-Non Finnish (NFE)

AF:

0.381

AC:

422193

AN:

1107676

Other (OTH)

AF:

0.371

AC:

22303

AN:

60140

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.437

Heterozygous variant carriers

16294

32587

48881

65174

81468

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13118

26236

39354

52472

65590

<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:

68496

AN:

151876

Hom.:

17659

Cov.:

AF XY:

0.444

AC XY:

32944

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.701

AC:

29021

AN:

41398

American (AMR)

AF:

0.318

AC:

4849

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.477

AC:

1653

AN:

3468

East Asian (EAS)

AF:

0.128

AC:

664

AN:

5168

South Asian (SAS)

AF:

0.200

AC:

964

AN:

4828

European-Finnish (FIN)

AF:

0.421

AC:

4425

AN:

10522

Middle Eastern (MID)

AF:

0.243

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.377

AC:

25624

AN:

67918

Other (OTH)

AF:

0.409

AC:

861

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1691

3382

5073

6764

8455

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:

0.393

Hom.:

31802

Bravo

AF:

0.458

TwinsUK

AF:

0.380

AC:

1409

ALSPAC

AF:

0.378

AC:

1458

ESP6500AA

AF:

0.698

AC:

3066

ESP6500EA

AF:

0.387

AC:

3324

ExAC

AF:

0.348

AC:

42244

Asia WGS

AF:

0.180

AC:

626

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

0.068

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.14

Eigen

Benign

-0.76

Eigen_PC

Benign

-0.82

FATHMM_MKL

Benign

0.070

LIST_S2

Benign

0.32

MetaRNN

Benign

0.0000034

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.0

PhyloP100

0.35

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.4

REVEL

Benign

0.13

Sift

Benign

0.13

Sift4G

Pathogenic

0.0

Polyphen

0.35

Vest4

0.058

MPC

0.011

ClinPred

0.0079

GERP RS

1.1

Varity_R

0.12

gMVP

0.45

Mutation Taster

=95/5

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