rs58477024
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_033034.3(TRIM5):c.327C>T(p.Asp109=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000257 in 1,613,460 control chromosomes in the GnomAD database, including 1 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 0.0011 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
TRIM5
NM_033034.3 synonymous
NM_033034.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0410
Genes affected
TRIM5 (HGNC:16276): (tripartite motif containing 5) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein forms homo-oligomers via the coilel-coil region and localizes to cytoplasmic bodies. It appears to function as a E3 ubiquitin-ligase and ubiqutinates itself to regulate its subcellular localization. It may play a role in retroviral restriction. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=0.041 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| TRIM5 | NM_033034.3 | c.327C>T | p.Asp109= | synonymous_variant | 2/8 | ENST00000380034.8 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRIM5 | ENST00000380034.8 | c.327C>T | p.Asp109= | synonymous_variant | 2/8 | 2 | NM_033034.3 | P1 |
Frequencies
GnomAD3 genomes 0.00112 AC: 169AN: 151478Hom.: 1 Cov.: 31
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GnomAD3 exomes AF: 0.000326 AC: 82AN: 251476Hom.: 0 AF XY: 0.000250 AC XY: 34AN XY: 135908
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GnomAD4 exome AF: 0.000167 AC: 244AN: 1461864Hom.: 0 Cov.: 35 AF XY: 0.000149 AC XY: 108AN XY: 727232
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GnomAD4 genome 0.00112 AC: 170AN: 151596Hom.: 1 Cov.: 31 AF XY: 0.00123 AC XY: 91AN XY: 74032
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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DANN
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RBP_binding_hub_radar
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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