16-3067563-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001376923.1(IL32):c.64A>C(p.Ile22Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00168 in 1,613,974 control chromosomes in the GnomAD database, including 19 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0064 ( 10 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 9 hom. )
Consequence
IL32
NM_001376923.1 missense
NM_001376923.1 missense
Scores
1
14
Clinical Significance
Conservation
PhyloP100: -3.80
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004904926).
BP6
?
Variant 16-3067563-A-C is Benign according to our data. Variant chr16-3067563-A-C is described in ClinVar as [Benign]. Clinvar id is 776965.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00642 (977/152220) while in subpopulation AFR AF= 0.0207 (861/41526). AF 95% confidence interval is 0.0196. There are 10 homozygotes in gnomad4. There are 453 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 10 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.64A>C | p.Ile22Leu | missense_variant | 4/7 | ENST00000525643.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IL32 | ENST00000525643.7 | c.64A>C | p.Ile22Leu | missense_variant | 4/7 | 1 | NM_001376923.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00638 AC: 970AN: 152102Hom.: 10 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00258 AC: 648AN: 251364Hom.: 6 AF XY: 0.00250 AC XY: 339AN XY: 135850
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GnomAD4 exome AF: 0.00119 AC: 1738AN: 1461754Hom.: 9 Cov.: 33 AF XY: 0.00133 AC XY: 968AN XY: 727186
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GnomAD4 genome ? AF: 0.00642 AC: 977AN: 152220Hom.: 10 Cov.: 32 AF XY: 0.00609 AC XY: 453AN XY: 74416
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ESP6500AA
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ExAC
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412
Asia WGS
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 29, 2018 | - - |
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
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
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
Uncertain
T
PROVEAN
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
REVEL
Benign
Sift
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
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
Polyphen
B;B;B;.;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;B;.;B;B;.;.
Vest4
MutPred
0.22
.;Gain of disorder (P = 0.1048);.;.;.;.;.;.;.;.;.;Gain of disorder (P = 0.1048);.;.;.;Gain of disorder (P = 0.1048);.;Gain of disorder (P = 0.1048);.;.;.;Gain of disorder (P = 0.1048);.;Gain of disorder (P = 0.1048);.;
MVP
MPC
0.11
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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