GeneBe

ENST00000409052.6:n.-273+2327C>T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000409052.6(IL1RN):​n.-472+1825T>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

GnomAD MNV: 𝑓 N/A
Genomes: 𝑓 N/A ( N/A hom., cov: )
Exomes 𝑓: N/A ( N/A hom. )

Consequence

IL1RN
ENST00000409052.6 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Publications

No publications found
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]
IL1RN Gene-Disease associations (from GenCC):
  • sterile multifocal osteomyelitis with periostitis and pustulosis
    Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, Labcorp Genetics (formerly Invitae), Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL1RNXM_011511121.2 linkc.-472+1825T>. intron_variant Intron 1 of 8 XP_011509423.1
IL1RNXM_047444184.1 linkc.-644+1825T>. intron_variant Intron 1 of 9 XP_047300140.1
IL1RNXM_047444185.1 linkc.-601+1825T>. intron_variant Intron 1 of 9 XP_047300141.1
IL1RNXM_047444186.1 linkc.-409+1825T>. intron_variant Intron 1 of 7 XP_047300142.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL1RNENST00000409052.6 linkn.-472+1825T>. intron_variant Intron 1 of 9 5 ENSP00000387210.1
IL1RNENST00000463073.6 linkn.103+1825T>. intron_variant Intron 1 of 3 5
IL1RNENST00000465812.6 linkn.275+1825T>. intron_variant Intron 1 of 5 5

Frequencies

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction

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

Publications

Other links and lift over

hg19: chr2-113858991; API