dbSNP rs3218977: IL1R2:c.*67A>G (chr2-102024739-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 ENST00000441002.1(IL1R2):c.*67A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,592,236 control chromosomes in the GnomAD database, including 19,659 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 0.15 ( 1825 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17834 hom. )

Consequence

IL1R2
ENST00000441002.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.951

Publications

25 publications found

Variant links:

Genes affected

IL1R2 (HGNC:5994): (interleukin 1 receptor type 2) The protein encoded by this gene is a cytokine receptor that belongs to the interleukin 1 receptor family. This protein binds interleukin alpha (IL1A), interleukin beta (IL1B), and interleukin 1 receptor, type I(IL1R1/IL1RA), and acts as a decoy receptor that inhibits the activity of its ligands. Interleukin 4 (IL4) is reported to antagonize the activity of interleukin 1 by inducing the expression and release of this cytokine. This gene and three other genes form a cytokine receptor gene cluster on chromosome 2q12. Alternative splicing results in multiple transcript variants and protein isoforms. Alternative splicing produces both membrane-bound and soluble proteins. A soluble protein is also produced by proteolytic cleavage. [provided by RefSeq, May 2012]

IL1R2 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R2	NM_004633.4 link	c.887+71A>G		intron_variant	Intron 7 of 8	ENST00000332549.8	NP_004624.1	P27930-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R2	ENST00000332549.8 link	c.887+71A>G		intron_variant	Intron 7 of 8	1	NM_004633.4	ENSP00000330959.3		P27930-1

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22444

AN:

152104

Hom.:

1818

Cov.:

show subpopulations

Gnomad AFR

AF:

0.144

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.134

Gnomad EAS

AF:

0.251

Gnomad SAS

AF:

0.274

Gnomad FIN

AF:

0.0977

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.155

GnomAD4 exome

AF:

0.153

AC:

220070

AN:

1440014

Hom.:

17834

Cov.:

AF XY:

0.156

AC XY:

111778

AN XY:

715246

show subpopulations

African (AFR)

AF:

0.135

AC:

4443

AN:

32850

American (AMR)

AF:

0.139

AC:

5957

AN:

42734

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

3201

AN:

25466

East Asian (EAS)

AF:

0.219

AC:

8595

AN:

39252

South Asian (SAS)

AF:

0.266

AC:

22538

AN:

84628

European-Finnish (FIN)

AF:

0.0995

AC:

5262

AN:

52872

Middle Eastern (MID)

AF:

0.156

AC:

869

AN:

5562

European-Non Finnish (NFE)

AF:

0.146

AC:

159762

AN:

1097318

Other (OTH)

AF:

0.159

AC:

9443

AN:

59332

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

8159

16319

24478

32638

40797

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.148

AC:

22467

AN:

152222

Hom.:

1825

Cov.:

AF XY:

0.150

AC XY:

11138

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.144

AC:

5981

AN:

41530

American (AMR)

AF:

0.156

AC:

2390

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.134

AC:

464

AN:

3466

East Asian (EAS)

AF:

0.251

AC:

1301

AN:

5186

South Asian (SAS)

AF:

0.274

AC:

1325

AN:

4830

European-Finnish (FIN)

AF:

0.0977

AC:

1035

AN:

10594

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9480

AN:

68018

Other (OTH)

AF:

0.163

AC:

344

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

967

1933

2900

3866

4833

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.143

Hom.:

7008

Bravo

AF:

0.148

Asia WGS

AF:

0.255

AC:

888

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.27

(source)

DANN

Benign

0.51

PhyloP100

-0.95

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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rs3218977

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