rs1057001
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021643.4(TRIB2):c.*858T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,286 control chromosomes in the GnomAD database, including 16,191 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 0.45 ( 16167 hom., cov: 33)
Exomes 𝑓: 0.57 ( 24 hom. )
Consequence
TRIB2
NM_021643.4 3_prime_UTR
NM_021643.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.406
Genes affected
TRIB2 (HGNC:30809): (tribbles pseudokinase 2) This gene encodes one of three members of the Tribbles family. The Tribbles members share a Trb domain, which is homologous to protein serine-threonine kinases, but lacks the active site lysine and probably lacks a catalytic function. The Tribbles proteins interact and modulate the activity of signal transduction pathways in a number of physiological and pathological processes. This Tribbles member induces apoptosis of cells mainly of the hematopoietic origin. It has been identified as a protein up-regulated by inflammatory stimuli in myeloid (THP-1) cells, and also as an oncogene that inactivates the transcription factor C/EBPalpha (CCAAT/enhancer-binding protein alpha) and causes acute myelogenous leukemia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2009]
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRIB2 | NM_021643.4 | c.*858T>A | 3_prime_UTR_variant | 3/3 | ENST00000155926.9 | ||
TRIB2 | NR_027303.2 | n.1695T>A | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIB2 | ENST00000155926.9 | c.*858T>A | 3_prime_UTR_variant | 3/3 | 1 | NM_021643.4 | P1 | ||
TRIB2 | ENST00000381465.2 | c.*858T>A | 3_prime_UTR_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.446 AC: 67864AN: 152036Hom.: 16152 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.568 AC: 75AN: 132Hom.: 24 Cov.: 0 AF XY: 0.565 AC XY: 52AN XY: 92
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GnomAD4 genome ? AF: 0.446 AC: 67909AN: 152154Hom.: 16167 Cov.: 33 AF XY: 0.452 AC XY: 33598AN XY: 74386
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at