rs4251985
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000259206.9(IL1RN):c.11-230G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,092 control chromosomes in the GnomAD database, including 4,107 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.21 ( 4107 hom., cov: 32)
Consequence
IL1RN
ENST00000259206.9 intron
ENST00000259206.9 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.153
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 2-113119836-G-T is Benign according to our data. Variant chr2-113119836-G-T is described in ClinVar as [Benign]. Clinvar id is 1232909.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL1RN | NM_000577.5 | c.10+1808G>T | intron_variant | ||||
IL1RN | NM_001318914.2 | c.-272-230G>T | intron_variant | ||||
IL1RN | NM_173841.3 | c.11-230G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206.9 | c.11-230G>T | intron_variant | 1 | |||||
IL1RN | ENST00000354115.6 | c.10+1808G>T | intron_variant | 1 | A1 | ||||
IL1RN | ENST00000361779.7 | c.-209-1612G>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.210 AC: 31888AN: 151974Hom.: 4101 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.210 AC: 31904AN: 152092Hom.: 4107 Cov.: 32 AF XY: 0.212 AC XY: 15791AN XY: 74330
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2021 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at