2-113117924-C-G
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The ENST00000259206(IL1RN):c.-95C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000065 in 814,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000065 ( 0 hom. )
Consequence
IL1RN
ENST00000259206 5_prime_UTR
ENST00000259206 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.129
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0000649 (43/662772) while in subpopulation NFE AF= 0.00011 (42/382546). AF 95% confidence interval is 0.0000831. There are 0 homozygotes in gnomad4_exome. There are 24 alleles in male gnomad4_exome subpopulation. Median coverage is 8. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | XM_011511121.2 | c.-272-2142C>G | intron_variant | XP_011509423.1 | ||||
IL1RN | XM_047444184.1 | c.-272-2142C>G | intron_variant | XP_047300140.1 | ||||
IL1RN | XM_047444185.1 | c.-273+259C>G | intron_variant | XP_047300141.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206 | c.-95C>G | 5_prime_UTR_variant | 1/6 | 1 | ENSP00000259206.5 | ||||
IL1RN | ENST00000354115 | c.-95C>G | 5_prime_UTR_variant | 1/5 | 1 | ENSP00000329072.3 | ||||
IL1RN | ENST00000361779 | c.-314C>G | 5_prime_UTR_variant | 1/6 | 1 | ENSP00000354816.3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000649 AC: 43AN: 662772Hom.: 0 Cov.: 8 AF XY: 0.0000669 AC XY: 24AN XY: 358888
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GnomAD4 genome AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74358
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autoinflammatory syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jan 06, 2017 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at