rs1180947
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_152268.4(PARS2):c.-30+780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0266 in 152,338 control chromosomes in the GnomAD database, including 100 homozygotes. 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 0.027 ( 100 hom., cov: 33)
Consequence
PARS2
NM_152268.4 intron
NM_152268.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.710
Genes affected
PARS2 (HGNC:30563): (prolyl-tRNA synthetase 2, mitochondrial) This gene encodes a putative member of the class II family of aminoacyl-tRNA synthetases. These enzymes play a critical role in protein biosynthesis by charging tRNAs with their cognate amino acids. This protein is encoded by the nuclear genome but is likely to be imported to the mitochondrion where it is thought to catalyze the ligation of proline to tRNA molecules. Mutations have been found in this gene in some patients with Alpers syndrome. [provided by RefSeq, Mar 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0266 (4051/152338) while in subpopulation SAS AF= 0.0435 (210/4830). AF 95% confidence interval is 0.0387. There are 100 homozygotes in gnomad4. There are 1927 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 100 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PARS2 | NM_152268.4 | c.-30+780T>C | intron_variant | ENST00000371279.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PARS2 | ENST00000371279.4 | c.-30+780T>C | intron_variant | 1 | NM_152268.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0266 AC: 4055AN: 152220Hom.: 100 Cov.: 33
GnomAD3 genomes
?
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4055
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152220
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0266 AC: 4051AN: 152338Hom.: 100 Cov.: 33 AF XY: 0.0259 AC XY: 1927AN XY: 74498
GnomAD4 genome
?
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4051
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152338
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33
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1927
AN XY:
74498
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66
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at