dbSNP rs2241132: IL1RL2:c.-12-281C>A (chr2-102187575-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003854.4(IL1RL2):c.-12-281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,022 control chromosomes in the GnomAD database, including 6,917 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

Frequency

Genomes: 𝑓 0.26 ( 6917 hom., cov: 32)

Consequence

IL1RL2
NM_003854.4 intron

Scores

Clinical Significance

association no assertion criteria provided O:1

Conservation

PhyloP100: -0.661

Publications

10 publications found

Variant links:

Genes affected

IL1RL2 (HGNC:5999): (interleukin 1 receptor like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. An experiment with transient gene expression demonstrated that this receptor was incapable of binding to interleukin 1 alpha and interleukin 1 beta with high affinity. This gene and four other interleukin 1 receptor family genes, including interleukin 1 receptor, type I (IL1R1), interleukin 1 receptor, type II (IL1R2), interleukin 1 receptor-like 1 (IL1RL1), and interleukin 18 receptor 1 (IL18R1), form a cytokine receptor gene cluster in a region mapped to chromosome 2q12. [provided by RefSeq, Jul 2008]

IL1RL2 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=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003854.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL1RL2	NM_003854.4	MANE Select	c.-12-281C>A	intron	N/A	NP_003845.2
IL1RL2	NM_001351446.2		c.-13+233C>A	intron	N/A	NP_001338375.1
IL1RL2	NM_001351447.1		c.69-281C>A	intron	N/A	NP_001338376.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL1RL2	ENST00000264257.7	TSL:1 MANE Select	c.-12-281C>A	intron	N/A	ENSP00000264257.2
IL1RL2	ENST00000441515.3	TSL:1	c.69-281C>A	intron	N/A	ENSP00000413348.2
IL1RL2	ENST00000421464.1	TSL:5	c.-13+233C>A	intron	N/A	ENSP00000387611.1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39236

AN:

151904

Hom.:

6900

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.152

Gnomad EAS

AF:

0.306

Gnomad SAS

AF:

0.0758

Gnomad FIN

AF:

0.182

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.135

Gnomad OTH

AF:

0.242

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

GnomAD4 genome

AF:

0.258

AC:

39288

AN:

152022

Hom.:

6917

Cov.:

AF XY:

0.259

AC XY:

19255

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.465

AC:

19267

AN:

41472

American (AMR)

AF:

0.371

AC:

5678

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.152

AC:

529

AN:

3472

East Asian (EAS)

AF:

0.306

AC:

1558

AN:

5096

South Asian (SAS)

AF:

0.0750

AC:

362

AN:

4826

European-Finnish (FIN)

AF:

0.182

AC:

1925

AN:

10598

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.135

AC:

9175

AN:

67958

Other (OTH)

AF:

0.240

AC:

506

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1353

2705

4058

5410

6763

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.175

Hom.:

1937

Bravo

AF:

0.293

Asia WGS

AF:

0.212

AC:

735

AN:

3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Ascending aortic dissection

Other:1

Feb 01, 2021

Beijing Anzhen Hospital, Capital Medical University

Significance:association

Review Status:no assertion criteria provided

Collection Method:case-control

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.2

(source)

DANN

Benign

0.56

PhyloP100

-0.66

PromoterAI

-0.11

Neutral

(source)

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over