Genetic Variant IL1R1:c.-83-12074C>T (chr2-102141867-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000409929.5(IL1R1):c.-83-12074C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,990 control chromosomes in the GnomAD database, including 14,829 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 0.41 ( 14822 hom., cov: 31)

Exomes 𝑓: 0.31 ( 7 hom. )

Consequence

IL1R1
ENST00000409929.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.34

Publications

40 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 (AFR) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409929.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein
IL1R1	NM_001320981.2	c.-135C>T	5_prime_UTR_premature_start_codon_gain	Exon 1 of 12	NP_001307910.1
IL1R1	NM_001320981.2	c.-135C>T	5_prime_UTR	Exon 1 of 12	NP_001307910.1
IL1R1	NM_001320978.2	c.-83-12074C>T	intron	N/A	NP_001307907.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IL1R1	ENST00000409929.5	TSL:1	c.-83-12074C>T	intron	N/A	ENSP00000386776.1
IL1R1	ENST00000428279.5	TSL:5	c.-581C>T	5_prime_UTR_premature_start_codon_gain	Exon 1 of 11	ENSP00000410461.1
IL1R1	ENST00000450319.5	TSL:3	c.-135C>T	5_prime_UTR_premature_start_codon_gain	Exon 1 of 5	ENSP00000411627.1

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62886

AN:

151792

Hom.:

14799

Cov.:

show subpopulations

Gnomad AFR

AF:

0.657

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.420

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.384

Gnomad FIN

AF:

0.270

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.315

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.313

AC:

AN:

Hom.:

Cov.:

AF XY:

0.271

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.557

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.415

AC:

62970

AN:

151910

Hom.:

14822

Cov.:

AF XY:

0.411

AC XY:

30528

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.657

AC:

27184

AN:

41376

American (AMR)

AF:

0.343

AC:

5246

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.420

AC:

1457

AN:

3468

East Asian (EAS)

AF:

0.316

AC:

1625

AN:

5136

South Asian (SAS)

AF:

0.383

AC:

1848

AN:

4820

European-Finnish (FIN)

AF:

0.270

AC:

2860

AN:

10578

Middle Eastern (MID)

AF:

0.439

AC:

129

AN:

294

European-Non Finnish (NFE)

AF:

0.315

AC:

21410

AN:

67924

Other (OTH)

AF:

0.393

AC:

829

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1667

3333

5000

6666

8333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

560

1120

1680

2240

2800

<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:

0.367

Hom.:

1459

Bravo

AF:

0.428

Asia WGS

AF:

0.374

AC:

1303

AN:

3478

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

0.67

PhyloP100

-1.3

PromoterAI

-0.061

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Computational scores

Splicing

Publications

Other links and lift over