rs11205384

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.13

Publications

0 publications found
Variant links:
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 21
    Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
  • Leigh syndrome
    Inheritance: AR Classification: LIMITED Submitted by: ClinGen

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TARS2NM_025150.5 linkc.775-1590C>G intron_variant Intron 7 of 17 ENST00000369064.8 NP_079426.2 Q9BW92-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TARS2ENST00000369064.8 linkc.775-1590C>G intron_variant Intron 7 of 17 1 NM_025150.5 ENSP00000358060.3 Q9BW92-1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151216
Hom.:
0
Cov.:
30
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
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:
0
AN:
151216
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
73794
African (AFR)
AF:
0.00
AC:
0
AN:
41174
American (AMR)
AF:
0.00
AC:
0
AN:
15224
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
3452
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5120
South Asian (SAS)
AF:
0.00
AC:
0
AN:
4790
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
10444
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
308
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
67718
Other (OTH)
AF:
0.00
AC:
0
AN:
2082

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.45
DANN
Benign
0.19
PhyloP100
-3.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11205384; hg19: chr1-150467368; API