16-3067422-C-CT
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001308078.4(IL32):c.62dupT(p.Leu22ProfsTer16) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,593,326 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000022 ( 1 hom. )
Consequence
IL32
NM_001308078.4 frameshift
NM_001308078.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -2.12
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;
BP6
Variant 16-3067422-C-CT is Benign according to our data. Variant chr16-3067422-C-CT is described in ClinVar as [Likely_benign]. Clinvar id is 726611.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
IL32 | NM_001376923.1 | c.54+8dupT | intron_variant | Intron 3 of 6 | ENST00000525643.7 | NP_001363852.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152056Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000296 AC: 7AN: 236816Hom.: 0 AF XY: 0.0000390 AC XY: 5AN XY: 128278
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GnomAD4 exome AF: 0.0000222 AC: 32AN: 1441270Hom.: 1 Cov.: 33 AF XY: 0.0000196 AC XY: 14AN XY: 715368
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GnomAD4 genome AF: 0.000230 AC: 35AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.000310 AC XY: 23AN XY: 74252
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 14, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at