rs4251955
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The XM_011511121.2(IL1RN):c.-273+3180G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0139 in 152,326 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.014 ( 44 hom., cov: 32)
Consequence
IL1RN
XM_011511121.2 intron
XM_011511121.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0280
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0139 (2113/152326) while in subpopulation AFR AF= 0.0483 (2008/41564). AF 95% confidence interval is 0.0466. There are 44 homozygotes in gnomad4. There are 979 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 44 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL1RN | XM_011511121.2 | c.-273+3180G>A | intron_variant | XP_011509423.1 | ||||
IL1RN | XM_047444184.1 | c.-273+3180G>A | intron_variant | XP_047300140.1 | ||||
IL1RN | XM_047444185.1 | c.-401-1243G>A | intron_variant | XP_047300141.1 | ||||
IL1RN | XM_047444186.1 | c.-210+3180G>A | intron_variant | XP_047300142.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
IL1RN | ENST00000409052.6 | c.-273+3180G>A | intron_variant, NMD_transcript_variant | 5 | ENSP00000387210 | |||||
IL1RN | ENST00000465812.6 | n.647-1243G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0139 AC: 2115AN: 152208Hom.: 44 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: 0.0139 AC: 2113AN: 152326Hom.: 44 Cov.: 32 AF XY: 0.0131 AC XY: 979AN XY: 74490
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ClinVar
Not reported inComputational 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