rs1365700579
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001040436.3(YARS2):āc.1106G>Cā(p.Cys369Ser) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,878 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001040436.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
YARS2 | NM_001040436.3 | c.1106G>C | p.Cys369Ser | missense_variant, splice_region_variant | 4/5 | ENST00000324868.13 | NP_001035526.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
YARS2 | ENST00000324868.13 | c.1106G>C | p.Cys369Ser | missense_variant, splice_region_variant | 4/5 | 1 | NM_001040436.3 | ENSP00000320658.8 | ||
YARS2 | ENST00000548490.1 | n.*117G>C | splice_region_variant, non_coding_transcript_exon_variant | 4/5 | 5 | ENSP00000447710.1 | ||||
YARS2 | ENST00000551673.5 | n.3G>C | non_coding_transcript_exon_variant | 1/3 | 5 | |||||
YARS2 | ENST00000548490.1 | n.*117G>C | 3_prime_UTR_variant | 4/5 | 5 | ENSP00000447710.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251400Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461768Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727180
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74298
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at