11-5680179-G-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_033034.3(TRIM5):c.-2C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 1,597,482 control chromosomes in the GnomAD database, including 231,342 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 0.43 ( 16359 hom., cov: 31)
Exomes 𝑓: 0.54 ( 214983 hom. )
Consequence
TRIM5
NM_033034.3 5_prime_UTR
NM_033034.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0950
Publications
35 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.435 AC: 66051AN: 151834Hom.: 16361 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
66051
AN:
151834
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.509 AC: 120882AN: 237290 AF XY: 0.522 show subpopulations
GnomAD2 exomes
AF:
AC:
120882
AN:
237290
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.541 AC: 782116AN: 1445528Hom.: 214983 Cov.: 52 AF XY: 0.544 AC XY: 390393AN XY: 717344 show subpopulations
GnomAD4 exome
AF:
AC:
782116
AN:
1445528
Hom.:
Cov.:
52
AF XY:
AC XY:
390393
AN XY:
717344
show subpopulations
African (AFR)
AF:
AC:
5578
AN:
33300
American (AMR)
AF:
AC:
21185
AN:
43912
Ashkenazi Jewish (ASJ)
AF:
AC:
13379
AN:
24710
East Asian (EAS)
AF:
AC:
17751
AN:
39572
South Asian (SAS)
AF:
AC:
49011
AN:
82946
European-Finnish (FIN)
AF:
AC:
27724
AN:
52664
Middle Eastern (MID)
AF:
AC:
3233
AN:
5684
European-Non Finnish (NFE)
AF:
AC:
613460
AN:
1102972
Other (OTH)
AF:
AC:
30795
AN:
59768
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.466
Heterozygous variant carriers
0
17340
34680
52021
69361
86701
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.435 AC: 66065AN: 151954Hom.: 16359 Cov.: 31 AF XY: 0.437 AC XY: 32444AN XY: 74240 show subpopulations
GnomAD4 genome
AF:
AC:
66065
AN:
151954
Hom.:
Cov.:
31
AF XY:
AC XY:
32444
AN XY:
74240
show subpopulations
African (AFR)
AF:
AC:
7571
AN:
41464
American (AMR)
AF:
AC:
6891
AN:
15268
Ashkenazi Jewish (ASJ)
AF:
AC:
1890
AN:
3466
East Asian (EAS)
AF:
AC:
2260
AN:
5146
South Asian (SAS)
AF:
AC:
2812
AN:
4808
European-Finnish (FIN)
AF:
AC:
5526
AN:
10550
Middle Eastern (MID)
AF:
AC:
141
AN:
292
European-Non Finnish (NFE)
AF:
AC:
37410
AN:
67940
Other (OTH)
AF:
AC:
1017
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1727
3453
5180
6906
8633
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1592
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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