rs141583132

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001376923.1(IL32):​c.200C>A​(p.Pro67Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

IL32
NM_001376923.1 missense, splice_region

Scores

2
17
Splicing: ADA: 0.00004936
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.51
Variant links:
Genes affected
IL32 (HGNC:16830): (interleukin 32) This gene encodes a member of the cytokine family. The protein contains a tyrosine sulfation site, 3 potential N-myristoylation sites, multiple putative phosphorylation sites, and an RGD cell-attachment sequence. Expression of this protein is increased after the activation of T-cells by mitogens or the activation of NK cells by IL-2. This protein induces the production of TNFalpha from macrophage cells. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.087097794).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL32NM_001376923.1 linkc.200C>A p.Pro67Gln missense_variant, splice_region_variant Exon 6 of 7 ENST00000525643.7 NP_001363852.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL32ENST00000525643.7 linkc.200C>A p.Pro67Gln missense_variant, splice_region_variant Exon 6 of 7 1 NM_001376923.1 ENSP00000432218.3 P24001-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1440868
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
714728
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.26
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
0.016
DANN
Benign
0.56
DEOGEN2
Benign
0.044
.;T;.;.;.;.;.;.;.;T;.;.;.;.;.;T;.;.;.;.;.;T;T;.;.;T;.
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0019
N
LIST_S2
Benign
0.51
.;.;T;.;.;.;.;.;.;T;.;.;.;.;.;.;T;.;T;.;T;T;T;T;T;T;T
M_CAP
Benign
0.0076
T
MetaRNN
Benign
0.087
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.86
T
MutationAssessor
Benign
0.0
.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;N;.;.;.;.;.;.;N;.;.;.;.
PrimateAI
Uncertain
0.54
T
PROVEAN
Benign
-1.9
N;N;N;D;N;N;N;D;N;N;N;N;N;N;N;N;N;N;D;N;D;N;N;N;N;N;N
REVEL
Benign
0.19
Sift
Uncertain
0.0060
D;D;D;D;D;D;D;D;D;D;D;T;D;D;T;D;T;T;D;D;D;D;D;D;T;T;T
Sift4G
Benign
0.33
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.90
P;P;.;P;P;P;P;P;P;.;P;.;P;P;.;P;.;.;.;P;P;.;P;P;.;.;.
Vest4
0.14
MutPred
0.30
.;Loss of loop (P = 0.0022);.;.;.;.;.;.;.;Loss of loop (P = 0.0022);.;.;.;.;.;Loss of loop (P = 0.0022);.;.;Loss of loop (P = 0.0022);.;.;.;Loss of loop (P = 0.0022);.;.;.;.;
MVP
0.41
MPC
0.35
ClinPred
0.15
T
GERP RS
-3.8
Varity_R
0.036
gMVP
0.0025

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.000049
dbscSNV1_RF
Benign
0.060
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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs141583132; hg19: chr16-3118239; API