rs730882155
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3_ModeratePP5
The NM_024678.6(NARS2):c.641C>T(p.Pro214Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000149 in 1,612,902 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P214T) has been classified as Uncertain significance.
Frequency
Consequence
NM_024678.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NARS2 | NM_024678.6 | c.641C>T | p.Pro214Leu | missense_variant | 6/14 | ENST00000281038.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NARS2 | ENST00000281038.10 | c.641C>T | p.Pro214Leu | missense_variant | 6/14 | 1 | NM_024678.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250754Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135540
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460748Hom.: 0 Cov.: 29 AF XY: 0.0000206 AC XY: 15AN XY: 726720
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74336
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 24 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at