NM_014438.5:c.261+789T>G
Variant names:
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
NM_014438.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.156
Publications
8 publications found
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]
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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 |
---|---|---|---|---|---|---|---|---|
IL36B | NM_014438.5 | c.261+789T>G | intron_variant | Intron 4 of 5 | ENST00000259213.9 | NP_055253.2 | ||
IL36B | NM_173178.3 | c.262-35T>G | intron_variant | Intron 4 of 4 | NP_775270.1 | |||
IL36B | XM_011510962.1 | c.262-35T>G | intron_variant | Intron 4 of 4 | XP_011509264.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152114Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
0
AN:
152114
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1419488Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 709002
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1419488
Hom.:
Cov.:
24
AF XY:
AC XY:
0
AN XY:
709002
African (AFR)
AF:
AC:
0
AN:
32428
American (AMR)
AF:
AC:
0
AN:
44452
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25816
East Asian (EAS)
AF:
AC:
0
AN:
39468
South Asian (SAS)
AF:
AC:
0
AN:
85406
European-Finnish (FIN)
AF:
AC:
0
AN:
53288
Middle Eastern (MID)
AF:
AC:
0
AN:
5652
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1074130
Other (OTH)
AF:
AC:
0
AN:
58848
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152114Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 74292
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
152114
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
74292
African (AFR)
AF:
AC:
0
AN:
41408
American (AMR)
AF:
AC:
0
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5186
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10586
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68042
Other (OTH)
AF:
AC:
0
AN:
2092
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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