dbSNP rs6749014: IL18R1:c.950-68C>T (chr2-102389988-C-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_003855.5(IL18R1):c.950-68C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,507,160 control chromosomes in the GnomAD database, including 178,125 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 ( 23587 hom., cov: 32)

Exomes 𝑓: 0.47 ( 154538 hom. )

Consequence

IL18R1
NM_003855.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.961

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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	UniProt
IL18R1	NM_003855.5	MANE Select	c.950-68C>T	intron	N/A	NP_003846.1	Q13478
IL18R1	NM_001371418.1		c.950-71C>T	intron	N/A	NP_001358347.1	B7ZKV7
IL18R1	NM_001371419.1		c.950-68C>T	intron	N/A	NP_001358348.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL18R1	ENST00000233957.7	TSL:5 MANE Select	c.950-68C>T	intron	N/A	ENSP00000233957.1	Q13478
IL18R1	ENST00000409599.5	TSL:5	c.950-68C>T	intron	N/A	ENSP00000387211.1	Q13478
IL18R1	ENST00000410040.5	TSL:2	c.950-68C>T	intron	N/A	ENSP00000386663.1	Q13478

Frequencies

GnomAD3 genomes

AF:

0.535

AC:

81224

AN:

151916

Hom.:

23556

Cov.:

show subpopulations

Gnomad AFR

AF:

0.732

Gnomad AMI

AF:

0.468

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.615

Gnomad EAS

AF:

0.150

Gnomad SAS

AF:

0.266

Gnomad FIN

AF:

0.543

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.526

GnomAD4 exome

AF:

0.467

AC:

632726

AN:

1355126

Hom.:

154538

AF XY:

0.460

AC XY:

310621

AN XY:

674604

show subpopulations

African (AFR)

AF:

0.747

AC:

23599

AN:

31572

American (AMR)

AF:

0.294

AC:

11932

AN:

40548

Ashkenazi Jewish (ASJ)

AF:

0.612

AC:

14886

AN:

24330

East Asian (EAS)

AF:

0.168

AC:

6489

AN:

38734

South Asian (SAS)

AF:

0.260

AC:

20950

AN:

80562

European-Finnish (FIN)

AF:

0.534

AC:

25731

AN:

48194

Middle Eastern (MID)

AF:

0.588

AC:

3253

AN:

5536

European-Non Finnish (NFE)

AF:

0.485

AC:

498799

AN:

1029048

Other (OTH)

AF:

0.479

AC:

27087

AN:

56602

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

15594

31189

46783

62378

77972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14428

28856

43284

57712

72140

<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:

0.535

AC:

81308

AN:

152034

Hom.:

23587

Cov.:

AF XY:

0.529

AC XY:

39276

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.732

AC:

30348

AN:

41458

American (AMR)

AF:

0.413

AC:

6314

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.615

AC:

2132

AN:

3468

East Asian (EAS)

AF:

0.150

AC:

778

AN:

5180

South Asian (SAS)

AF:

0.266

AC:

1279

AN:

4812

European-Finnish (FIN)

AF:

0.543

AC:

5723

AN:

10546

Middle Eastern (MID)

AF:

0.548

AC:

161

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33045

AN:

67970

Other (OTH)

AF:

0.522

AC:

1101

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1761

3523

5284

7046

8807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.494

Hom.:

4843

Bravo

AF:

0.535

Asia WGS

AF:

0.232

AC:

809

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.12

(source)

DANN

Benign

0.77

PhyloP100

-0.96

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