chr13-30630989-A-G
Variant names:
Variant summary
Our verdict is . The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
Uncertain significance
The NM_001321532.2(USPL1):c.-161A>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
USPL1
NM_001321532.2 5_prime_UTR_premature_start_codon_gain
NM_001321532.2 5_prime_UTR_premature_start_codon_gain
Scores
1
18
Clinical Significance
Conservation
PhyloP100: 1.19
Publications
0 publications found
Genes affected
USPL1 (HGNC:20294): (ubiquitin specific peptidase like 1) Enables SUMO binding activity and SUMO-specific isopeptidase activity. Involved in several processes, including Cajal body organization; protein desumoylation; and snRNA transcription. Located in Cajal body. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript NM_001321532.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.031).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001321532.2. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| USPL1 | MANE Select | c.383A>G | p.Tyr128Cys | missense | Exon 4 of 9 | NP_005791.3 | |||
| USPL1 | c.-161A>G | 5_prime_UTR_premature_start_codon_gain | Exon 3 of 8 | NP_001308461.1 | |||||
| USPL1 | c.-161A>G | 5_prime_UTR | Exon 3 of 8 | NP_001308461.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| USPL1 | TSL:1 MANE Select | c.383A>G | p.Tyr128Cys | missense | Exon 4 of 9 | ENSP00000255304.4 | Q5W0Q7-1 | ||
| USPL1 | TSL:1 | c.-119-6755A>G | intron | N/A | ENSP00000480656.1 | Q5W0Q7-2 | |||
| USPL1 | c.383A>G | p.Tyr128Cys | missense | Exon 4 of 9 | ENSP00000568193.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461768Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727190 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1461768
Hom.:
Cov.:
31
AF XY:
AC XY:
2
AN XY:
727190
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26132
East Asian (EAS)
AF:
AC:
0
AN:
39692
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53314
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1112006
Other (OTH)
AF:
AC:
0
AN:
60394
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.450
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Varity_R
gMVP
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
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.