11-5678194-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_033034.3(TRIM5):c.744+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,594,250 control chromosomes in the GnomAD database, including 17 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0057 ( 7 hom., cov: 33)
Exomes 𝑓: 0.00059 ( 10 hom. )
Consequence
TRIM5
NM_033034.3 intron
NM_033034.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.31
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 11-5678194-C-T is Benign according to our data. Variant chr11-5678194-C-T is described in ClinVar as [Benign]. Clinvar id is 730591.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00571 (869/152284) while in subpopulation AFR AF= 0.0203 (844/41556). AF 95% confidence interval is 0.0192. There are 7 homozygotes in gnomad4. There are 396 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRIM5 | NM_033034.3 | c.744+10G>A | intron_variant | ENST00000380034.8 | NP_149023.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRIM5 | ENST00000380034.8 | c.744+10G>A | intron_variant | 2 | NM_033034.3 | ENSP00000369373.3 | ||||
ENSG00000239920 | ENST00000380259.7 | n.231+10G>A | intron_variant | 5 | ENSP00000369609.3 |
Frequencies
GnomAD3 genomes AF: 0.00571 AC: 869AN: 152166Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.00152 AC: 371AN: 243388Hom.: 5 AF XY: 0.00114 AC XY: 150AN XY: 131658
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GnomAD4 exome AF: 0.000586 AC: 845AN: 1441966Hom.: 10 Cov.: 30 AF XY: 0.000503 AC XY: 360AN XY: 715164
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GnomAD4 genome AF: 0.00571 AC: 869AN: 152284Hom.: 7 Cov.: 33 AF XY: 0.00532 AC XY: 396AN XY: 74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 16, 2018 | - - |
Computational 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
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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