rs10489341
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025228.4(TRAF3IP3):c.-159-258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,870 control chromosomes in the GnomAD database, including 2,025 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.10 ( 2022 hom., cov: 32)
Exomes 𝑓: 0.023 ( 3 hom. )
Consequence
TRAF3IP3
NM_025228.4 intron
NM_025228.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.50
Genes affected
TRAF3IP3 (HGNC:30766): (TRAF3 interacting protein 3) The gene encodes a protein that mediates cell growth by modulating the c-Jun N-terminal kinase signal transduction pathway. The encoded protein may also interact with a large multi-protein assembly containing the phosphatase 2A catalytic subunit. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP3 | NM_025228.4 | c.-159-258C>T | intron_variant | ENST00000367025.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP3 | ENST00000367025.8 | c.-159-258C>T | intron_variant | 1 | NM_025228.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.103 AC: 15597AN: 151998Hom.: 2022 Cov.: 32
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GnomAD4 exome AF: 0.0225 AC: 17AN: 754Hom.: 3 Cov.: 0 AF XY: 0.0231 AC XY: 13AN XY: 562
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GnomAD4 genome ? AF: 0.103 AC: 15620AN: 152116Hom.: 2022 Cov.: 32 AF XY: 0.0992 AC XY: 7378AN XY: 74366
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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