rs369116355
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001376923.1(IL32):c.142-10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000929 in 1,603,912 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000091 ( 0 hom. )
Consequence
IL32
NM_001376923.1 intron
NM_001376923.1 intron
Scores
2
Splicing: ADA: 0.00003428
2
Clinical Significance
Conservation
PhyloP100: -1.19
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.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
Variant 16-3068170-C-T is Benign according to our data. Variant chr16-3068170-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 755756.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.142-10C>T | intron_variant | Intron 5 of 6 | ENST00000525643.7 | NP_001363852.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000104 AC: 24AN: 230738Hom.: 0 AF XY: 0.000120 AC XY: 15AN XY: 124540
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GnomAD4 exome AF: 0.0000909 AC: 132AN: 1451752Hom.: 0 Cov.: 31 AF XY: 0.0000970 AC XY: 70AN XY: 721332
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GnomAD4 genome AF: 0.000112 AC: 17AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74354
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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
Jul 05, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at