Genetic Variant IL1R2:c.-61-7773T>C (chr2-102000742-T-C) – 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.-61-7773T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 150,900 control chromosomes in the GnomAD database, including 13,612 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 0.43 ( 13612 hom., cov: 31)

Consequence

IL1R2
NM_004633.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.601

Publications

20 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R2	NM_004633.4 link	c.-61-7773T>C		intron_variant	Intron 1 of 8	ENST00000332549.8	NP_004624.1	P27930-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
IL1R2	ENST00000332549.8 link	c.-61-7773T>C	intron_variant	Intron 1 of 8	1	NM_004633.4	ENSP00000330959.3	P27930-1
IL1R2	ENST00000393414.6 link	c.-62+1626T>C	intron_variant	Intron 1 of 8	1		ENSP00000377066.2	P27930-1
IL1R2	ENST00000464994.5 link	n.75-7773T>C	intron_variant	Intron 1 of 2	3
IL1R2	ENST00000493749.1 link	n.53-7773T>C	intron_variant	Intron 1 of 2	2

Frequencies

GnomAD3 genomes

AF:

0.429

AC:

64733

AN:

150782

Hom.:

13597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.458

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.556

Gnomad MID

AF:

0.327

Gnomad NFE

AF:

0.396

Gnomad OTH

AF:

0.416

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.429

AC:

64796

AN:

150900

Hom.:

13612

Cov.:

AF XY:

0.437

AC XY:

32275

AN XY:

73804

show subpopulations

African (AFR)

AF:

0.453

AC:

18642

AN:

41138

American (AMR)

AF:

0.445

AC:

6754

AN:

15168

Ashkenazi Jewish (ASJ)

AF:

0.337

AC:

1159

AN:

3440

East Asian (EAS)

AF:

0.458

AC:

2348

AN:

5130

South Asian (SAS)

AF:

0.426

AC:

2038

AN:

4788

European-Finnish (FIN)

AF:

0.556

AC:

5843

AN:

10510

Middle Eastern (MID)

AF:

0.345

AC:

100

AN:

290

European-Non Finnish (NFE)

AF:

0.396

AC:

26707

AN:

67448

Other (OTH)

AF:

0.419

AC:

874

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

1738

3476

5214

6952

8690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.408

Hom.:

40145

Bravo

AF:

0.431

Asia WGS

AF:

0.452

AC:

1573

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.1

(source)

DANN

Benign

0.60

PhyloP100

-0.60

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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2-102000742-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over