NM_001311175.2:c.-109_-101dupCGCCGCCCG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001311175.2(TNFAIP8L3):c.-109_-101dupCGCCGCCCG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000532 in 1,062,408 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00061 ( 2 hom., cov: 27)
Exomes 𝑓: 0.00052 ( 2 hom. )
Consequence
TNFAIP8L3
NM_001311175.2 5_prime_UTR
NM_001311175.2 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0640
Genes affected
TNFAIP8L3 (HGNC:20620): (TNF alpha induced protein 8 like 3) Predicted to enable phosphatidylinositol binding activity and phosphatidylinositol transfer activity. Predicted to be involved in several processes, including inositol lipid-mediated signaling; positive regulation of intracellular signal transduction; and positive regulation of phosphatidylinositol 3-kinase activity. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High Homozygotes in GnomAd4 at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFAIP8L3 | NM_001311175.2 | c.-109_-101dupCGCCGCCCG | 5_prime_UTR_variant | Exon 1 of 2 | ENST00000637513.2 | NP_001298104.1 | ||
TNFAIP8L3 | NM_207381.4 | c.173-17_173-9dupCGCCGCCCG | intron_variant | Intron 1 of 2 | NP_997264.2 | |||
MIR4713HG | NR_146310.1 | n.194+57029_194+57037dupGGCGCGGGC | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFAIP8L3 | ENST00000637513.2 | c.-109_-101dupCGCCGCCCG | 5_prime_UTR_variant | Exon 1 of 2 | 1 | NM_001311175.2 | ENSP00000489743.1 | |||
TNFAIP8L3 | ENST00000327536.5 | c.173-17_173-9dupCGCCGCCCG | intron_variant | Intron 1 of 2 | 1 | ENSP00000328016.5 | ||||
MIR4713HG | ENST00000559909.1 | n.194+57029_194+57037dupGGCGCGGGC | intron_variant | Intron 1 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000606 AC: 89AN: 146826Hom.: 2 Cov.: 27
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GnomAD4 exome AF: 0.000519 AC: 475AN: 915474Hom.: 2 Cov.: 4 AF XY: 0.000554 AC XY: 238AN XY: 429590
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GnomAD4 genome AF: 0.000613 AC: 90AN: 146934Hom.: 2 Cov.: 27 AF XY: 0.000503 AC XY: 36AN XY: 71506
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at