2-112917503-A-G
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014439.4(IL37):c.266-132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 963,232 control chromosomes in the GnomAD database, including 452,516 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 0.91 ( 64006 hom., cov: 31)
Exomes 𝑓: 0.98 ( 388510 hom. )
Consequence
IL37
NM_014439.4 intron
NM_014439.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.56
Genes affected
IL37 (HGNC:15563): (interleukin 37) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine can bind to, and may be a ligand for interleukin 18 receptor (IL18R1/IL-1Rrp). This cytokine also binds to interleukin 18 binding protein (IL18BP), an inhibitory binding protein of interleukin 18 (IL18), and subsequently forms a complex with IL18 receptor beta subunit, and through which it inhibits the activity of IL18. This gene along with eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. Five alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL37 | NM_014439.4 | c.266-132A>G | intron_variant | ENST00000263326.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL37 | ENST00000263326.8 | c.266-132A>G | intron_variant | 1 | NM_014439.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.909 AC: 138161AN: 152056Hom.: 63979 Cov.: 31
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GnomAD4 exome AF: 0.977 AC: 792439AN: 811058Hom.: 388510 AF XY: 0.976 AC XY: 404410AN XY: 414502
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GnomAD4 genome ? AF: 0.908 AC: 138231AN: 152174Hom.: 64006 Cov.: 31 AF XY: 0.909 AC XY: 67654AN XY: 74400
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at