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:

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=-0.82).

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1R1	NM_000877.4 link	c.487-140T>A		intron_variant	Intron 5 of 11	ENST00000410023.6	NP_000868.1	P14778

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1R1	ENST00000410023.6 link	c.487-140T>A		intron_variant	Intron 5 of 11	1	NM_000877.4	ENSP00000386380.1		P14778

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over