dbSNP rs3819370: IL1R2:c.513+61A>G (chr2-102016112-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_004633.4(IL1R2):c.513+61A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 1,323,420 control chromosomes in the GnomAD database, including 14,520 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 0.17 ( 2607 hom., cov: 32)

Exomes 𝑓: 0.13 ( 11913 hom. )

Consequence

IL1R2
NM_004633.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.728

Publications

8 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R2	NM_004633.4 link	c.513+61A>G		intron_variant	Intron 4 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.513+61A>G		intron_variant	Intron 4 of 8	1	NM_004633.4	ENSP00000330959.3		P27930-1

Frequencies

GnomAD3 genomes

AF:

0.169

AC:

25734

AN:

152016

Hom.:

2603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.266

Gnomad AMI

AF:

0.0943

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.118

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.148

GnomAD4 exome

AF:

0.128

AC:

150210

AN:

1171286

Hom.:

11913

Cov.:

AF XY:

0.130

AC XY:

76596

AN XY:

588628

show subpopulations

African (AFR)

AF:

0.271

AC:

7284

AN:

26860

American (AMR)

AF:

0.181

AC:

6675

AN:

36974

Ashkenazi Jewish (ASJ)

AF:

0.122

AC:

2815

AN:

23086

East Asian (EAS)

AF:

0.316

AC:

11474

AN:

36284

South Asian (SAS)

AF:

0.205

AC:

15084

AN:

73626

European-Finnish (FIN)

AF:

0.182

AC:

9145

AN:

50218

Middle Eastern (MID)

AF:

0.167

AC:

858

AN:

5138

European-Non Finnish (NFE)

AF:

0.103

AC:

89578

AN:

869120

Other (OTH)

AF:

0.146

AC:

7297

AN:

49980

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

6076

12152

18227

24303

30379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3308

6616

9924

13232

16540

<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:

0.169

AC:

25775

AN:

152134

Hom.:

2607

Cov.:

AF XY:

0.173

AC XY:

12893

AN XY:

74372

show subpopulations

African (AFR)

AF:

0.266

AC:

11030

AN:

41474

American (AMR)

AF:

0.156

AC:

2386

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.118

AC:

409

AN:

3470

East Asian (EAS)

AF:

0.286

AC:

1482

AN:

5180

South Asian (SAS)

AF:

0.213

AC:

1025

AN:

4814

European-Finnish (FIN)

AF:

0.172

AC:

1815

AN:

10580

Middle Eastern (MID)

AF:

0.136

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7183

AN:

68020

Other (OTH)

AF:

0.151

AC:

319

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1051

2103

3154

4206

5257

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.149

Hom.:

267

Bravo

AF:

0.173

Asia WGS

AF:

0.279

AC:

968

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

1.4

(source)

DANN

Benign

0.36

PhyloP100

-0.73

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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