rs11205384
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong
The NM_025150.5(TARS2):c.775-1590C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 30)
Failed GnomAD Quality Control
Consequence
TARS2
NM_025150.5 intron
NM_025150.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.13
Publications
0 publications found
Genes affected
TARS2 (HGNC:30740): (threonyl-tRNA synthetase 2, mitochondrial) This gene encodes a member of the class-II aminoacyl-tRNA synthetase family. The encoded protein is a mitochondrial aminoacyl-tRNA synthetase. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 4. [provided by RefSeq, Dec 2012]
TARS2 Gene-Disease associations (from GenCC):
- combined oxidative phosphorylation defect type 21Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
- Leigh syndromeInheritance: AR Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 151216Hom.: 0 Cov.: 30
GnomAD3 genomes
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30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151216Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 73794
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151216
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
73794
African (AFR)
AF:
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0
AN:
41174
American (AMR)
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0
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15224
Ashkenazi Jewish (ASJ)
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0
AN:
3452
East Asian (EAS)
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0
AN:
5120
South Asian (SAS)
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AC:
0
AN:
4790
European-Finnish (FIN)
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0
AN:
10444
Middle Eastern (MID)
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AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67718
Other (OTH)
AF:
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0
AN:
2082
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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