rs540848445
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_025265.4(TSEN2):c.-98_-96delAGC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.008 in 152,376 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0080 ( 5 hom., cov: 33)
Exomes 𝑓: 0.014 ( 0 hom. )
Consequence
TSEN2
NM_025265.4 5_prime_UTR
NM_025265.4 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.248
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]
TSEN2 Gene-Disease associations (from GenCC):
- pontocerebellar hypoplasia type 2BInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia
- pontocerebellar hypoplasia type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP6
Variant 3-12484797-TGCA-T is Benign according to our data. Variant chr3-12484797-TGCA-T is described in ClinVar as Benign. ClinVar VariationId is 2653539.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00799 (1216/152166) while in subpopulation NFE AF = 0.0133 (904/67990). AF 95% confidence interval is 0.0126. There are 5 homozygotes in GnomAd4. There are 546 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
BS2
High Homozygotes in GnomAd4 at 5 AR gene
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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TSEN2 | NM_025265.4 | MANE Select | c.-98_-96delAGC | 5_prime_UTR | Exon 1 of 12 | NP_079541.1 | Q8NCE0-1 | ||
| TSEN2 | NM_001321279.2 | c.-98_-96delAGC | 5_prime_UTR | Exon 1 of 11 | NP_001308208.1 | Q8NCE0-3 | |||
| TSEN2 | NM_001321278.2 | c.-18+283_-18+285delAGC | intron | N/A | NP_001308207.1 | C9J7Z4 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TSEN2 | ENST00000284995.11 | TSL:1 MANE Select | c.-98_-96delAGC | 5_prime_UTR | Exon 1 of 12 | ENSP00000284995.6 | Q8NCE0-1 | ||
| TSEN2 | ENST00000402228.7 | TSL:1 | c.-18+172_-18+174delAGC | intron | N/A | ENSP00000385976.3 | Q8NCE0-1 | ||
| TSEN2 | ENST00000454502.6 | TSL:1 | c.-18+283_-18+285delAGC | intron | N/A | ENSP00000392029.2 | Q8NCE0-4 |
Frequencies
GnomAD3 genomes 0.00802 AC: 1220AN: 152048Hom.: 6 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1220
AN:
152048
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.0143 AC: 3AN: 210Hom.: 0 AF XY: 0.0179 AC XY: 3AN XY: 168 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
210
Hom.:
AF XY:
AC XY:
3
AN XY:
168
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
6
East Asian (EAS)
AF:
AC:
0
AN:
2
South Asian (SAS)
AF:
AC:
0
AN:
2
European-Finnish (FIN)
AF:
AC:
0
AN:
2
Middle Eastern (MID)
AF:
AC:
0
AN:
2
European-Non Finnish (NFE)
AF:
AC:
2
AN:
178
Other (OTH)
AF:
AC:
0
AN:
14
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00799 AC: 1216AN: 152166Hom.: 5 Cov.: 33 AF XY: 0.00734 AC XY: 546AN XY: 74412 show subpopulations
GnomAD4 genome
AF:
AC:
1216
AN:
152166
Hom.:
Cov.:
33
AF XY:
AC XY:
546
AN XY:
74412
show subpopulations
African (AFR)
AF:
AC:
102
AN:
41518
American (AMR)
AF:
AC:
120
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
31
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5150
South Asian (SAS)
AF:
AC:
9
AN:
4826
European-Finnish (FIN)
AF:
AC:
31
AN:
10610
Middle Eastern (MID)
AF:
AC:
3
AN:
294
European-Non Finnish (NFE)
AF:
AC:
904
AN:
67990
Other (OTH)
AF:
AC:
16
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
67
133
200
266
333
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<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.:
Bravo
AF:
Asia WGS
AF:
AC:
12
AN:
3478
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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