rs774367638

Variant summary

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

The NM_001376923.1(IL32):​c.137T>A​(p.Leu46Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

IL32
NM_001376923.1 missense

Scores

2
4
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0750
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]

Genome browser will be placed here

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=0.15071899).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IL32NM_001376923.1 linkc.137T>A p.Leu46Gln missense_variant Exon 5 of 7 ENST00000525643.7 NP_001363852.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IL32ENST00000525643.7 linkc.137T>A p.Leu46Gln missense_variant Exon 5 of 7 1 NM_001376923.1 ENSP00000432218.3 P24001-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251372
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135884
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461832
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
727218
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
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
Pathogenic
0.77
BayesDel_addAF
Uncertain
0.034
T
BayesDel_noAF
Benign
-0.11
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Benign
0.044
.;T;T;.;.;T;.;.;.;.;.;T;.;.;.;.;.;T;.;.;.;T;T;.;.;.
Eigen
Benign
-0.55
Eigen_PC
Benign
-0.78
FATHMM_MKL
Benign
0.016
N
LIST_S2
Benign
0.33
.;.;T;T;.;.;.;.;.;.;.;T;.;.;.;.;.;.;T;.;T;T;T;T;T;T
M_CAP
Benign
0.041
D
MetaRNN
Benign
0.15
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
-0.75
T
MutationAssessor
Benign
0.0
.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;N;.;.;.;.;N;.;.;.
PrimateAI
Benign
0.46
T
PROVEAN
Uncertain
-2.8
D;D;.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;N
REVEL
Benign
0.25
Sift
Uncertain
0.020
D;D;.;D;D;D;D;D;D;D;D;D;D;T;D;D;T;D;D;D;D;D;D;D;T;T
Sift4G
Pathogenic
0.0
D;D;T;T;D;T;D;D;D;D;D;D;D;T;D;D;T;D;D;D;D;D;D;D;T;T
Polyphen
1.0
D;D;D;.;D;D;D;D;D;D;D;.;D;.;D;D;.;D;.;D;D;.;D;D;.;.
Vest4
0.42
MutPred
0.38
.;Gain of disorder (P = 0.0254);.;.;.;.;.;.;.;.;.;Gain of disorder (P = 0.0254);.;.;.;.;.;Gain of disorder (P = 0.0254);Gain of disorder (P = 0.0254);.;.;.;Gain of disorder (P = 0.0254);.;.;.;
MVP
0.83
MPC
0.33
ClinPred
0.46
T
GERP RS
0.78
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.0
Varity_R
0.31
gMVP
0.0066

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

LitVar

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

Other links and lift over

dbSNP: rs774367638; hg19: chr16-3118007; API