rs2307859
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001270508.2(TNFAIP3):c.296-15_296-13del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 1,603,882 control chromosomes in the GnomAD database, including 322,124 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.51 ( 23464 hom., cov: 0)
Exomes 𝑓: 0.64 ( 298660 hom. )
Consequence
TNFAIP3
NM_001270508.2 intron
NM_001270508.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.282
Genes affected
TNFAIP3 (HGNC:11896): (TNF alpha induced protein 3) This gene was identified as a gene whose expression is rapidly induced by the tumor necrosis factor (TNF). The protein encoded by this gene is a zinc finger protein and ubiqitin-editing enzyme, and has been shown to inhibit NF-kappa B activation as well as TNF-mediated apoptosis. The encoded protein, which has both ubiquitin ligase and deubiquitinase activities, is involved in the cytokine-mediated immune and inflammatory responses. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 6-137874824-TCTC-T is Benign according to our data. Variant chr6-137874824-TCTC-T is described in ClinVar as [Benign]. Clinvar id is 993326.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFAIP3 | NM_001270508.2 | c.296-15_296-13del | intron_variant | ENST00000612899.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFAIP3 | ENST00000612899.5 | c.296-15_296-13del | intron_variant | 5 | NM_001270508.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 77779AN: 151574Hom.: 23466 Cov.: 0
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GnomAD3 exomes AF: 0.615 AC: 151478AN: 246108Hom.: 48869 AF XY: 0.626 AC XY: 83189AN XY: 132970
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GnomAD4 exome AF: 0.635 AC: 922830AN: 1452188Hom.: 298660 AF XY: 0.638 AC XY: 459894AN XY: 721190
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GnomAD4 genome ? AF: 0.513 AC: 77781AN: 151694Hom.: 23464 Cov.: 0 AF XY: 0.517 AC XY: 38342AN XY: 74092
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2019 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan | Nov 12, 2023 | This variant is classified as Benign based on local population frequency. This variant was detected in 79% of patients studied by a panel of primary immunodeficiencies. Number of patients: 76. Only high quality variants are reported. - |
Autoinflammatory syndrome, familial, Behcet-like Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Autoinflammatory syndrome, familial, Behcet-like 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 29, 2023 | - - |
Computational scores
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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