GeneBe

rs1685626921

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_012275.3(IL36RN):​c.30-18C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,441,900 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: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

IL36RN
NM_012275.3 intron

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.179

Publications

0 publications found
Variant links:
Genes affected
IL36RN (HGNC:15561): (interleukin 36 receptor antagonist) The protein encoded by this gene is a member of the interleukin 1 cytokine family. This cytokine was shown to specifically inhibit the activation of NF-kappaB induced by interleukin 1 family, member 6 (IL1F6). This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. Two alternatively spliced transcript variants encoding the same protein have been reported. [provided by RefSeq, Jul 2008]
IL36RN Gene-Disease associations (from GenCC):
  • psoriasis 14, pustular
    Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, G2P, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
  • pustulosis palmaris et plantaris
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 2-113060834-C-A is Benign according to our data. Variant chr2-113060834-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2796130.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL36RNNM_012275.3 linkc.30-18C>A intron_variant Intron 2 of 4 ENST00000393200.7 NP_036407.1 Q9UBH0A0A024R518
IL36RNNM_173170.1 linkc.30-18C>A intron_variant Intron 2 of 4 NP_775262.1 Q9UBH0A0A024R518
IL36RNXM_047443918.1 linkc.30-18C>A intron_variant Intron 3 of 5 XP_047299874.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL36RNENST00000393200.7 linkc.30-18C>A intron_variant Intron 2 of 4 1 NM_012275.3 ENSP00000376896.2 Q9UBH0
IL36RNENST00000346807.7 linkc.30-18C>A intron_variant Intron 2 of 4 1 ENSP00000259212.3 Q9UBH0
IL36RNENST00000437409.2 linkc.30-18C>A intron_variant Intron 1 of 3 1 ENSP00000409262.2 Q9UBH0C9JTH1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.94e-7
AC:
1
AN:
1441900
Hom.:
0
Cov.:
29
AF XY:
0.00000139
AC XY:
1
AN XY:
718564
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33096
American (AMR)
AF:
0.00
AC:
0
AN:
44636
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25976
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39594
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85750
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53386
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5610
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1094178
Other (OTH)
AF:
0.0000168
AC:
1
AN:
59674
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0
Bravo
AF:
0.00000378

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Generalized pustular psoriasis Benign:1
Nov 27, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
CADD
Benign
7.5
DANN
Benign
0.77
PhyloP100
0.18

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1685626921; hg19: chr2-113818411; API