2-113118042-A-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_173841.3(IL1RN):c.10+14A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,611,104 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000013 ( 0 hom. )
Consequence
IL1RN
NM_173841.3 intron
NM_173841.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.408
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 -8 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 2-113118042-A-C is Benign according to our data. Variant chr2-113118042-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2050355.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000138 (21/152214) while in subpopulation AFR AF= 0.000506 (21/41526). AF 95% confidence interval is 0.000338. There are 0 homozygotes in gnomad4. There are 12 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | NM_173841.3 | c.10+14A>C | intron_variant | Intron 1 of 5 | NP_776213.1 | |||
IL1RN | NM_000577.5 | c.10+14A>C | intron_variant | Intron 1 of 4 | NP_000568.1 | |||
IL1RN | NM_001318914.2 | c.-273+14A>C | intron_variant | Intron 1 of 6 | NP_001305843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000259206.9 | c.10+14A>C | intron_variant | Intron 1 of 5 | 1 | ENSP00000259206.5 | ||||
IL1RN | ENST00000354115.6 | c.10+14A>C | intron_variant | Intron 1 of 4 | 1 | ENSP00000329072.3 | ||||
IL1RN | ENST00000361779.7 | c.-210+14A>C | intron_variant | Intron 1 of 5 | 1 | ENSP00000354816.3 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152096Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251482Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135916
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1458890Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12AN XY: 725904
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152214Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74422
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Sterile multifocal osteomyelitis with periostitis and pustulosis Benign:1
Dec 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at