2-113028150-A-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_014438.5(IL36B):​c.261+789T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

IL36B
NM_014438.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.156

Publications

8 publications found
Variant links:
Genes affected
IL36B (HGNC:15564): (interleukin 36 beta) The protein encoded by this gene is a member of the interleukin 1 cytokine family. Protein structure modeling indicated that this cytokine may contain a 12-stranded beta-trefoil structure that is conserved between IL1A (IL-A alpha) and IL1B (IL-1 beta). This gene and eight other interleukin 1 family genes form a cytokine gene cluster on chromosome 2. Two alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL36BNM_014438.5 linkc.261+789T>G intron_variant Intron 4 of 5 ENST00000259213.9 NP_055253.2 Q9NZH7-1
IL36BNM_173178.3 linkc.262-35T>G intron_variant Intron 4 of 4 NP_775270.1 Q9NZH7-2
IL36BXM_011510962.1 linkc.262-35T>G intron_variant Intron 4 of 4 XP_011509264.1 Q9NZH7-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL36BENST00000259213.9 linkc.261+789T>G intron_variant Intron 4 of 5 1 NM_014438.5 ENSP00000259213.4 Q9NZH7-1
IL36BENST00000327407.2 linkc.262-35T>G intron_variant Intron 4 of 4 1 ENSP00000328420.2 Q9NZH7-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
152114
Hom.:
0
Cov.:
30
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1419488
Hom.:
0
Cov.:
24
AF XY:
0.00
AC XY:
0
AN XY:
709002
African (AFR)
AF:
0.00
AC:
0
AN:
32428
American (AMR)
AF:
0.00
AC:
0
AN:
44452
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25816
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39468
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85406
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
53288
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5652
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
1074130
Other (OTH)
AF:
0.00
AC:
0
AN:
58848
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
152114
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
74292
African (AFR)
AF:
0.00
AC:
0
AN:
41408
American (AMR)
AF:
0.00
AC:
0
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3472
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5186
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10586
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
68042
Other (OTH)
AF:
0.00
AC:
0
AN:
2092

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.55
DANN
Benign
0.66
PhyloP100
-0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs1562304; hg19: chr2-113785727; API