rs1491196550
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_025265.4(TSEN2):c.910-168_910-167insGT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.034 ( 52 hom., cov: 0)
Consequence
TSEN2
NM_025265.4 intron
NM_025265.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.376
Publications
0 publications found
Genes affected
TSEN2 (HGNC:28422): (tRNA splicing endonuclease subunit 2) This gene encodes one of the subunits of the tRNA splicing endonuclease. This endonuclease catalyzes the first step in RNA splicing which is the removal of introns. Mutations in this gene have been associated with pontocerebellar hypoplasia type 2. A pseudogene has been identified on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 3-12516442-A-ATG is Benign according to our data. Variant chr3-12516442-A-ATG is described in ClinVar as Likely_benign. ClinVar VariationId is 1202067.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0513 is higher than 0.05.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_025265.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TSEN2 | TSL:1 MANE Select | c.910-169_910-168insTG | intron | N/A | ENSP00000284995.6 | Q8NCE0-1 | |||
| TSEN2 | TSL:1 | c.910-169_910-168insTG | intron | N/A | ENSP00000385976.3 | Q8NCE0-1 | |||
| TSEN2 | TSL:1 | c.733-169_733-168insTG | intron | N/A | ENSP00000392029.2 | Q8NCE0-4 |
Frequencies
GnomAD3 genomes 0.0340 AC: 3025AN: 89056Hom.: 51 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
3025
AN:
89056
Hom.:
Cov.:
0
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.0340 AC: 3031AN: 89134Hom.: 52 Cov.: 0 AF XY: 0.0339 AC XY: 1449AN XY: 42792 show subpopulations
GnomAD4 genome
AF:
AC:
3031
AN:
89134
Hom.:
Cov.:
0
AF XY:
AC XY:
1449
AN XY:
42792
show subpopulations
African (AFR)
AF:
AC:
1316
AN:
24492
American (AMR)
AF:
AC:
272
AN:
7220
Ashkenazi Jewish (ASJ)
AF:
AC:
21
AN:
2278
East Asian (EAS)
AF:
AC:
2
AN:
2808
South Asian (SAS)
AF:
AC:
61
AN:
2528
European-Finnish (FIN)
AF:
AC:
118
AN:
5982
Middle Eastern (MID)
AF:
AC:
1
AN:
166
European-Non Finnish (NFE)
AF:
AC:
1191
AN:
41776
Other (OTH)
AF:
AC:
49
AN:
1170
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.490
Heterozygous variant carriers
0
134
268
401
535
669
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
32
64
96
128
160
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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