dbSNP rs11465702: IL18RAP:c.796+55A>G (chr2-102441432-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_001393487.1(IL18RAP):c.796+55A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 1,383,484 control chromosomes in the GnomAD database, including 13,148 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 0.11 ( 1174 hom., cov: 32)

Exomes 𝑓: 0.13 ( 11974 hom. )

Consequence

IL18RAP
NM_001393487.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52

Publications

15 publications found

Variant links:

Genes affected

IL18RAP (HGNC:5989): (interleukin 18 receptor accessory protein) The protein encoded by this gene is an accessory subunit of the heterodimeric receptor for interleukin 18 (IL18), a proinflammatory cytokine involved in inducing cell-mediated immunity. This protein enhances the IL18-binding activity of the IL18 receptor and plays a role in signaling by IL18. Mutations in this gene are associated with Crohn's disease and inflammatory bowel disease, and susceptibility to celiac disease and leprosy. Alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Feb 2014]

IL18RAP 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 (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL18RAP	NM_001393487.1 link	c.796+55A>G		intron_variant	Intron 5 of 9	ENST00000687160.1	NP_001380416.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
IL18RAP	ENST00000687160.1 link	c.796+55A>G	intron_variant	Intron 5 of 9		NM_001393487.1	ENSP00000510345.1
IL18RAP	ENST00000264260.6 link	c.796+55A>G	intron_variant	Intron 7 of 11	1		ENSP00000264260.2
IL18RAP	ENST00000409369.1 link	c.370+55A>G	intron_variant	Intron 5 of 9	1		ENSP00000387201.1

Frequencies

GnomAD3 genomes

AF:

0.115

AC:

17507

AN:

152126

Hom.:

1174

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0647

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.211

Gnomad EAS

AF:

0.0142

Gnomad SAS

AF:

0.0656

Gnomad FIN

AF:

0.174

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.125

GnomAD4 exome

AF:

0.133

AC:

163994

AN:

1231240

Hom.:

11974

AF XY:

0.132

AC XY:

81968

AN XY:

623160

show subpopulations

African (AFR)

AF:

0.0671

AC:

1935

AN:

28840

American (AMR)

AF:

0.0763

AC:

3248

AN:

42594

Ashkenazi Jewish (ASJ)

AF:

0.222

AC:

5406

AN:

24324

East Asian (EAS)

AF:

0.00799

AC:

306

AN:

38286

South Asian (SAS)

AF:

0.0576

AC:

4618

AN:

80200

European-Finnish (FIN)

AF:

0.170

AC:

8986

AN:

52786

Middle Eastern (MID)

AF:

0.127

AC:

670

AN:

5276

European-Non Finnish (NFE)

AF:

0.146

AC:

132043

AN:

906338

Other (OTH)

AF:

0.129

AC:

6782

AN:

52596

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

6648

13297

19945

26594

33242

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4174

8348

12522

16696

20870

<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:

0.115

AC:

17507

AN:

152244

Hom.:

1174

Cov.:

AF XY:

0.114

AC XY:

8494

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0647

AC:

2687

AN:

41556

American (AMR)

AF:

0.102

AC:

1563

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.211

AC:

732

AN:

3470

East Asian (EAS)

AF:

0.0143

AC:

AN:

5182

South Asian (SAS)

AF:

0.0657

AC:

317

AN:

4826

European-Finnish (FIN)

AF:

0.174

AC:

1848

AN:

10598

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.145

AC:

9866

AN:

68012

Other (OTH)

AF:

0.122

AC:

258

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

779

1557

2336

3114

3893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

376

564

752

940

<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:

0.135

Hom.:

1904

Bravo

AF:

0.107

Asia WGS

AF:

0.0380

AC:

134

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

5.4

(source)

DANN

Benign

0.47

PhyloP100

1.5

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