rs904918193
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2PM4
The NM_207346.3(TSEN54):c.17_22delAGCCCG(p.Glu6_Pro7del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000622 in 1,124,830 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000031 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000030 ( 0 hom. )
Consequence
TSEN54
NM_207346.3 disruptive_inframe_deletion
NM_207346.3 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.14
Publications
0 publications found
Genes affected
TSEN54 (HGNC:27561): (tRNA splicing endonuclease subunit 54) This gene encodes a subunit of the tRNA splicing endonuclease complex, which catalyzes the removal of introns from precursor tRNAs. The complex is also implicated in pre-mRNA 3-prime end processing. Mutations in this gene result in pontocerebellar hypoplasia type 2.[provided by RefSeq, Oct 2009]
TSEN54 Gene-Disease associations (from GenCC):
- pontocerebellar hypoplasia type 2AInheritance: AR Classification: STRONG Submitted by: PanelApp Australia
- pontocerebellar hypoplasia type 4Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, PanelApp Australia
- pontocerebellar hypoplasia type 5Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- pontocerebellar hypoplasia type 2Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_207346.3.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_207346.3. 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 |
|---|---|---|---|---|---|---|---|---|---|
| TSEN54 | NM_207346.3 | MANE Select | c.17_22delAGCCCG | p.Glu6_Pro7del | disruptive_inframe_deletion | Exon 1 of 11 | NP_997229.2 | Q7Z6J9-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TSEN54 | ENST00000333213.11 | TSL:1 MANE Select | c.17_22delAGCCCG | p.Glu6_Pro7del | disruptive_inframe_deletion | Exon 1 of 11 | ENSP00000327487.6 | Q7Z6J9-1 | |
| TSEN54 | ENST00000680999.1 | c.17_22delAGCCCG | p.Glu6_Pro7del | disruptive_inframe_deletion | Exon 1 of 11 | ENSP00000504984.1 | A0A7P0Z413 | ||
| TSEN54 | ENST00000915433.1 | c.17_22delAGCCCG | p.Glu6_Pro7del | disruptive_inframe_deletion | Exon 1 of 11 | ENSP00000585492.1 |
Frequencies
GnomAD3 genomes 0.0000231 AC: 3AN: 129752Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
3
AN:
129752
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
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Gnomad ASJ
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Gnomad EAS
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Gnomad FIN
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Gnomad NFE
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Gnomad OTH
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GnomAD4 exome AF: 0.00000302 AC: 3AN: 994982Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 468316 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
994982
Hom.:
AF XY:
AC XY:
0
AN XY:
468316
show subpopulations
African (AFR)
AF:
AC:
2
AN:
19752
American (AMR)
AF:
AC:
0
AN:
5514
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
10612
East Asian (EAS)
AF:
AC:
0
AN:
17218
South Asian (SAS)
AF:
AC:
0
AN:
18780
European-Finnish (FIN)
AF:
AC:
0
AN:
16394
Middle Eastern (MID)
AF:
AC:
0
AN:
2448
European-Non Finnish (NFE)
AF:
AC:
1
AN:
866800
Other (OTH)
AF:
AC:
0
AN:
37464
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
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1
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2
3
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome 0.0000308 AC: 4AN: 129848Hom.: 0 Cov.: 33 AF XY: 0.0000473 AC XY: 3AN XY: 63448 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
4
AN:
129848
Hom.:
Cov.:
33
AF XY:
AC XY:
3
AN XY:
63448
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
4
AN:
34748
American (AMR)
AF:
AC:
0
AN:
13222
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2994
East Asian (EAS)
AF:
AC:
0
AN:
5144
South Asian (SAS)
AF:
AC:
0
AN:
4074
European-Finnish (FIN)
AF:
AC:
0
AN:
8494
Middle Eastern (MID)
AF:
AC:
0
AN:
250
European-Non Finnish (NFE)
AF:
AC:
0
AN:
58344
Other (OTH)
AF:
AC:
0
AN:
1800
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00400497), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.375
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
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0.60
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0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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Age
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ClinVar
Not reported inComputational 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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