rs202059991
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_012275.3(IL36RN):āc.436A>Gā(p.Ile146Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000781 in 1,612,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012275.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL36RN | NM_012275.3 | c.436A>G | p.Ile146Val | missense_variant | 5/5 | ENST00000393200.7 | |
IL36RN | NM_173170.1 | c.436A>G | p.Ile146Val | missense_variant | 5/5 | ||
IL36RN | XM_047443918.1 | c.436A>G | p.Ile146Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL36RN | ENST00000393200.7 | c.436A>G | p.Ile146Val | missense_variant | 5/5 | 1 | NM_012275.3 | P1 | |
IL36RN | ENST00000346807.7 | c.436A>G | p.Ile146Val | missense_variant | 5/5 | 1 | P1 | ||
IL36RN | ENST00000437409.2 | c.436A>G | p.Ile146Val | missense_variant | 4/4 | 1 | P1 | ||
IL36RN | ENST00000514072.1 | c.127A>G | p.Ile43Val | missense_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000148 AC: 37AN: 250222Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135384
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460448Hom.: 0 Cov.: 32 AF XY: 0.0000895 AC XY: 65AN XY: 726630
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74298
ClinVar
Submissions by phenotype
Generalized pustular psoriasis Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Deficiency of the interleukin-36 receptor antagonist Other:1
not provided, no classification provided | phenotyping only | GenomeConnect - Invitae Patient Insights Network | - | Variant classified as Likely benign and reported on 10-31-2018 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at