dbSNP rs3213732: IL18R1:c.688+137A>G (chr2-102381819-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_003855.5(IL18R1):c.688+137A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 654,156 control chromosomes in the GnomAD database, including 79,439 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 0.53 ( 23532 hom., cov: 31)

Exomes 𝑓: 0.45 ( 55907 hom. )

Consequence

IL18R1
NM_003855.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.592

Publications

13 publications found

Variant links:

Genes affected

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:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003855.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL18R1	NM_003855.5	MANE Select	c.688+137A>G	intron	N/A	NP_003846.1
IL18R1	NM_001371418.1		c.688+137A>G	intron	N/A	NP_001358347.1
IL18R1	NM_001371419.1		c.688+137A>G	intron	N/A	NP_001358348.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL18R1	ENST00000233957.7	TSL:5 MANE Select	c.688+137A>G	intron	N/A	ENSP00000233957.1
IL18R1	ENST00000409599.5	TSL:5	c.688+137A>G	intron	N/A	ENSP00000387211.1
IL18R1	ENST00000410040.5	TSL:2	c.688+137A>G	intron	N/A	ENSP00000386663.1

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

81084

AN:

151840

Hom.:

23500

Cov.:

show subpopulations

Gnomad AFR

AF:

0.731

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.613

Gnomad EAS

AF:

0.151

Gnomad SAS

AF:

0.265

Gnomad FIN

AF:

0.541

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.525

GnomAD4 exome

AF:

0.455

AC:

228265

AN:

502198

Hom.:

55907

AF XY:

0.443

AC XY:

117817

AN XY:

265772

show subpopulations

African (AFR)

AF:

0.743

AC:

9728

AN:

13092

American (AMR)

AF:

0.343

AC:

6932

AN:

20218

Ashkenazi Jewish (ASJ)

AF:

0.608

AC:

8769

AN:

14418

East Asian (EAS)

AF:

0.173

AC:

5161

AN:

29882

South Asian (SAS)

AF:

0.258

AC:

12275

AN:

47528

European-Finnish (FIN)

AF:

0.533

AC:

19301

AN:

36204

Middle Eastern (MID)

AF:

0.576

AC:

1229

AN:

2134

European-Non Finnish (NFE)

AF:

0.487

AC:

151997

AN:

311920

Other (OTH)

AF:

0.480

AC:

12873

AN:

26802

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

5527

11054

16580

22107

27634

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1496

2992

4488

5984

7480

<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:

0.534

AC:

81169

AN:

151958

Hom.:

23532

Cov.:

AF XY:

0.528

AC XY:

39205

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.731

AC:

30269

AN:

41418

American (AMR)

AF:

0.413

AC:

6311

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

2130

AN:

3472

East Asian (EAS)

AF:

0.151

AC:

780

AN:

5174

South Asian (SAS)

AF:

0.265

AC:

1277

AN:

4818

European-Finnish (FIN)

AF:

0.541

AC:

5701

AN:

10534

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33013

AN:

67936

Other (OTH)

AF:

0.521

AC:

1100

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1746

3492

5239

6985

8731

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.520

Hom.:

2771

Bravo

AF:

0.535

Asia WGS

AF:

0.232

AC:

808

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.6

(source)

DANN

Benign

0.37

PhyloP100

0.59

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over