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:

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=-0.86).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL18R1	NM_003855.5 link	c.688+137A>G		intron_variant	Intron 6 of 10	ENST00000233957.7	NP_003846.1	Q13478

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL18R1	ENST00000233957.7 link	c.688+137A>G	intron_variant	Intron 6 of 10	5	NM_003855.5	ENSP00000233957.1	Q13478
IL18R1	ENST00000409599.5 link	c.688+137A>G	intron_variant	Intron 7 of 11	5		ENSP00000387211.1	Q13478
IL18R1	ENST00000410040.5 link	c.688+137A>G	intron_variant	Intron 6 of 10	2		ENSP00000386663.1	Q13478
IL18R1	ENST00000677287.1 link	n.*232+137A>G	intron_variant	Intron 6 of 10			ENSP00000503023.1	Q86YL8

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

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

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 v4.3

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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rs3213732

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