rs2637988

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000259206.9(IL1RN):​c.11-864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 152,050 control chromosomes in the GnomAD database, including 22,037 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 0.53 ( 22037 hom., cov: 32)

Consequence

IL1RN
ENST00000259206.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0830
Variant links:
Genes affected
IL1RN (HGNC:6000): (interleukin 1 receptor antagonist) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This protein inhibits the activities of interleukin 1, alpha (IL1A) and interleukin 1, beta (IL1B), and modulates a variety of interleukin 1 related immune and inflammatory responses, particularly in the acute phase of infection and inflammation. This gene and five other closely related cytokine genes form a gene cluster spanning approximately 400 kb on chromosome 2. A polymorphism of this gene is reported to be associated with increased risk of osteoporotic fractures and gastric cancer. Several alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Aug 2020]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IL1RNNM_000577.5 linkuse as main transcriptc.10+1174G>A intron_variant NP_000568.1
IL1RNNM_001318914.2 linkuse as main transcriptc.-272-864G>A intron_variant NP_001305843.1
IL1RNNM_173841.3 linkuse as main transcriptc.11-864G>A intron_variant NP_776213.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IL1RNENST00000259206.9 linkuse as main transcriptc.11-864G>A intron_variant 1 ENSP00000259206 P18510-3
IL1RNENST00000354115.6 linkuse as main transcriptc.10+1174G>A intron_variant 1 ENSP00000329072 A1P18510-2
IL1RNENST00000361779.7 linkuse as main transcriptc.-210+1174G>A intron_variant 1 ENSP00000354816 P18510-4

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
81061
AN:
151934
Hom.:
22027
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.441
Gnomad AMI
AF:
0.602
Gnomad AMR
AF:
0.548
Gnomad ASJ
AF:
0.597
Gnomad EAS
AF:
0.409
Gnomad SAS
AF:
0.555
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.598
Gnomad NFE
AF:
0.603
Gnomad OTH
AF:
0.550
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.533
AC:
81112
AN:
152050
Hom.:
22037
Cov.:
32
AF XY:
0.528
AC XY:
39225
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.441
Gnomad4 AMR
AF:
0.547
Gnomad4 ASJ
AF:
0.597
Gnomad4 EAS
AF:
0.410
Gnomad4 SAS
AF:
0.556
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.603
Gnomad4 OTH
AF:
0.551
Alfa
AF:
0.588
Hom.:
12209
Bravo
AF:
0.536
Asia WGS
AF:
0.482
AC:
1677
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.6
DANN
Benign
0.58

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2637988; hg19: chr2-113876779; API