dbSNP rs5743658: IL18BP:c.-1307A>C (chr11-71998678-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000497194.6(IL18BP):c.-1307A>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 153,162 control chromosomes in the GnomAD database, including 2,749 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 0.13 ( 2747 hom., cov: 32)

Exomes 𝑓: 0.033 ( 2 hom. )

Consequence

IL18BP
ENST00000497194.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

5 publications found

Variant links:

Genes affected

IL18BP (HGNC:5987): (interleukin 18 binding protein) The protein encoded by this gene functions as an inhibitor of the proinflammatory cytokine, IL18. It binds IL18, prevents the binding of IL18 to its receptor, and thus inhibits IL18-induced IFN-gamma production, resulting in reduced T-helper type 1 immune responses. This protein is constitutively expressed and secreted in mononuclear cells. Elevated level of this protein is detected in the intestinal tissues of patients with Crohn's disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Feb 2011]

IL18BP Gene-Disease associations (from GenCC):

hepatitis, fulminant viral, susceptibility to
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

IL18BP 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=-0.88).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL18BP	NM_001039660.2 link	c.-400A>C		upstream_gene_variant		ENST00000393703.9	NP_001034749.1	O95998-2A0A024R5G2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL18BP	ENST00000393703.9 link	c.-400A>C		upstream_gene_variant		3	NM_001039660.2	ENSP00000377306.4		O95998-2

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19153

AN:

151984

Hom.:

2724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.353

Gnomad AMI

AF:

0.0570

Gnomad AMR

AF:

0.0655

Gnomad ASJ

AF:

0.0472

Gnomad EAS

AF:

0.0741

Gnomad SAS

AF:

0.0427

Gnomad FIN

AF:

0.0245

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0330

Gnomad OTH

AF:

0.0972

GnomAD4 exome

AF:

0.0330

AC:

AN:

1060

Hom.:

Cov.:

AF XY:

0.0361

AC XY:

AN XY:

638

show subpopulations

African (AFR)

AF:

0.333

AC:

AN:

American (AMR)

AF:

0.0244

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.214

AC:

AN:

South Asian (SAS)

AF:

0.0204

AC:

AN:

196

European-Finnish (FIN)

AF:

0.0750

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0297

AC:

AN:

640

Other (OTH)

AF:

0.0323

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.126

AC:

19223

AN:

152102

Hom.:

2747

Cov.:

AF XY:

0.123

AC XY:

9116

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.354

AC:

14683

AN:

41460

American (AMR)

AF:

0.0655

AC:

1001

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.0472

AC:

164

AN:

3472

East Asian (EAS)

AF:

0.0735

AC:

380

AN:

5168

South Asian (SAS)

AF:

0.0432

AC:

208

AN:

4818

European-Finnish (FIN)

AF:

0.0245

AC:

260

AN:

10604

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0330

AC:

2246

AN:

67986

Other (OTH)

AF:

0.0957

AC:

202

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

703

1407

2110

2814

3517

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

190

380

570

760

950

<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:

0.0684

Hom.:

1327

Bravo

AF:

0.140

Asia WGS

AF:

0.0720

AC:

253

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.7

(source)

DANN

Benign

0.73

PhyloP100

-1.8

PromoterAI

0.0080

Neutral

(source)

Mutation Taster

=300/0

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