dbSNP rs997049: IL1R1:c.487-140T>A (chr2-102165973-T-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_000877.4(IL1R1):c.487-140T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 638,552 control chromosomes in the GnomAD database, including 43,249 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 0.31 ( 8188 hom., cov: 32)

Exomes 𝑓: 0.37 ( 35061 hom. )

Consequence

IL1R1
NM_000877.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00200

Publications

11 publications found

Variant links:

Genes affected

IL1R1 (HGNC:5993): (interleukin 1 receptor type 1) This gene encodes a cytokine receptor that belongs to the interleukin-1 receptor family. The encoded protein is a receptor for interleukin-1 alpha, interleukin-1 beta, and interleukin-1 receptor antagonist. It is an important mediator involved in many cytokine-induced immune and inflammatory responses. This gene is located in a cluster of related cytokine receptor genes on chromosome 2q12. [provided by RefSeq, Dec 2013]

IL1R1 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=-0.82).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000877.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL1R1	NM_000877.4	MANE Select	c.487-140T>A	intron	N/A	NP_000868.1	P14778
IL1R1	NM_001320978.2		c.487-140T>A	intron	N/A	NP_001307907.1	P14778
IL1R1	NM_001320980.2		c.487-140T>A	intron	N/A	NP_001307909.1	P14778

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
IL1R1	ENST00000410023.6	TSL:1 MANE Select	c.487-140T>A	intron	N/A	ENSP00000386380.1	P14778
IL1R1	ENST00000409929.5	TSL:1	c.487-140T>A	intron	N/A	ENSP00000386776.1	B8ZZW4
IL1R1	ENST00000853658.1		c.487-140T>A	intron	N/A	ENSP00000523717.1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47328

AN:

151926

Hom.:

8187

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.454

Gnomad AMR

AF:

0.274

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.391

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.390

Gnomad OTH

AF:

0.323

GnomAD4 exome

AF:

0.373

AC:

181369

AN:

486508

Hom.:

35061

AF XY:

0.373

AC XY:

94265

AN XY:

253036

show subpopulations

African (AFR)

AF:

0.145

AC:

1878

AN:

12972

American (AMR)

AF:

0.252

AC:

4373

AN:

17354

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

4090

AN:

12950

East Asian (EAS)

AF:

0.377

AC:

11499

AN:

30520

South Asian (SAS)

AF:

0.360

AC:

13974

AN:

38818

European-Finnish (FIN)

AF:

0.403

AC:

15121

AN:

37502

Middle Eastern (MID)

AF:

0.277

AC:

550

AN:

1984

European-Non Finnish (NFE)

AF:

0.391

AC:

120399

AN:

308064

Other (OTH)

AF:

0.360

AC:

9485

AN:

26344

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

5211

10423

15634

20846

26057

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1518

3036

4554

6072

7590

<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:

0.311

AC:

47333

AN:

152044

Hom.:

8188

Cov.:

AF XY:

0.312

AC XY:

23184

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.151

AC:

6260

AN:

41500

American (AMR)

AF:

0.273

AC:

4167

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.322

AC:

1115

AN:

3468

East Asian (EAS)

AF:

0.431

AC:

2231

AN:

5182

South Asian (SAS)

AF:

0.366

AC:

1763

AN:

4816

European-Finnish (FIN)

AF:

0.391

AC:

4123

AN:

10544

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.390

AC:

26482

AN:

67962

Other (OTH)

AF:

0.328

AC:

691

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1600

3200

4801

6401

8001

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

488

976

1464

1952

2440

<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:

0.358

Hom.:

1412

Bravo

AF:

0.295

Asia WGS

AF:

0.391

AC:

1357

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.0

(source)

DANN

Benign

0.65

PhyloP100

-0.0020

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over