rs1057990
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015836.4(WARS2):c.*302A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 370,524 control chromosomes in the GnomAD database, including 14,563 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 0.29 ( 7256 hom., cov: 33)
Exomes 𝑓: 0.25 ( 7307 hom. )
Consequence
WARS2
NM_015836.4 3_prime_UTR
NM_015836.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.202
Genes affected
WARS2 (HGNC:12730): (tryptophanyl tRNA synthetase 2, mitochondrial) Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. Two forms of tryptophanyl-tRNA synthetase exist, a cytoplasmic form, named WARS, and a mitochondrial form, named WARS2. This gene encodes the mitochondrial tryptophanyl-tRNA synthetase. Two alternative transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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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=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WARS2 | NM_015836.4 | c.*302A>G | 3_prime_UTR_variant | 6/6 | ENST00000235521.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WARS2 | ENST00000235521.5 | c.*302A>G | 3_prime_UTR_variant | 6/6 | 1 | NM_015836.4 | P1 | ||
WARS2 | ENST00000369426.9 | c.*751A>G | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.295 AC: 44805AN: 151936Hom.: 7248 Cov.: 33
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GnomAD4 exome AF: 0.247 AC: 53913AN: 218470Hom.: 7307 Cov.: 0 AF XY: 0.246 AC XY: 27940AN XY: 113698
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GnomAD4 genome ? AF: 0.295 AC: 44845AN: 152054Hom.: 7256 Cov.: 33 AF XY: 0.290 AC XY: 21526AN XY: 74324
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at