rs587777213
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PM5PP3_Moderate
The NM_001040436.3(YARS2):c.137G>T(p.Gly46Val) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G46D) has been classified as Pathogenic.
Frequency
Consequence
NM_001040436.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YARS2 | ENST00000324868.13 | c.137G>T | p.Gly46Val | missense_variant | Exon 1 of 5 | 1 | NM_001040436.3 | ENSP00000320658.8 | ||
YARS2 | ENST00000548490.1 | n.59G>T | non_coding_transcript_exon_variant | Exon 1 of 5 | 5 | ENSP00000447710.1 | ||||
ENSG00000286950 | ENST00000666291.1 | n.229C>A | non_coding_transcript_exon_variant | Exon 1 of 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461692Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727160
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.