16-3069090-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001376923.1(IL32):c.302G>T(p.Gly101Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000053 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000069 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
IL32
NM_001376923.1 missense
NM_001376923.1 missense
Scores
16
Clinical Significance
Conservation
PhyloP100: -2.40
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 Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.044130802).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.302G>T | p.Gly101Val | missense_variant | 7/7 | ENST00000525643.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL32 | ENST00000525643.7 | c.302G>T | p.Gly101Val | missense_variant | 7/7 | 1 | NM_001376923.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152154Hom.: 0 Cov.: 34
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?
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GnomAD3 exomes AF: 0.0000222 AC: 5AN: 225690Hom.: 0 AF XY: 0.0000243 AC XY: 3AN XY: 123520
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000687 AC: 10AN: 1456658Hom.: 0 Cov.: 53 AF XY: 0.00000828 AC XY: 6AN XY: 724214
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.0000525 AC: 8AN: 152272Hom.: 0 Cov.: 34 AF XY: 0.0000403 AC XY: 3AN XY: 74472
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 25, 2022 | The c.302G>T (p.G101V) alteration is located in exon 8 (coding exon 6) of the IL32 gene. This alteration results from a G to T substitution at nucleotide position 302, causing the glycine (G) at amino acid position 101 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
M_CAP
Benign
T
MetaRNN
Benign
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;T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;D;.;D;N;D;N;N;N;N;N;D;N;D;N;N;D;D;D;N;N;N;D;D;N;D;D;N;D
REVEL
Benign
Sift
Benign
T;D;.;T;D;T;T;T;T;D;T;T;T;T;T;T;T;D;T;T;T;D;T;D;T;T;D;T;T
Sift4G
Benign
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;T;T
Polyphen
B;B;B;.;B;B;B;B;B;B;B;.;B;.;B;B;.;B;.;.;B;B;.;B;B;.;.;.;.
Vest4
MutPred
0.20
.;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
MPC
0.48
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at