chr2-113117640-A-C
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The XM_047444185.1(IL1RN):c.-298A>C variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 399,516 control chromosomes in the GnomAD database, including 9,897 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.21 ( 4101 hom., cov: 33)
Exomes 𝑓: 0.20 ( 5796 hom. )
Consequence
IL1RN
XM_047444185.1 5_prime_UTR_premature_start_codon_gain
XM_047444185.1 5_prime_UTR_premature_start_codon_gain
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.28
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 2-113117640-A-C is Benign according to our data. Variant chr2-113117640-A-C is described in ClinVar as [Benign]. Clinvar id is 1249883.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | XM_047444185.1 | c.-298A>C | 5_prime_UTR_premature_start_codon_gain_variant | Exon 4 of 10 | XP_047300141.1 | |||
IL1RN | XM_047444185.1 | c.-298A>C | 5_prime_UTR_variant | Exon 4 of 10 | XP_047300141.1 | |||
IL1RN | XM_011511121.2 | c.-272-2426A>C | intron_variant | Intron 3 of 8 | XP_011509423.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.209 AC: 31855AN: 152122Hom.: 4095 Cov.: 33
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GnomAD4 exome AF: 0.205 AC: 50645AN: 247276Hom.: 5796 Cov.: 0 AF XY: 0.205 AC XY: 26300AN XY: 128232
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GnomAD4 genome AF: 0.209 AC: 31870AN: 152240Hom.: 4101 Cov.: 33 AF XY: 0.212 AC XY: 15811AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
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Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at