rs587777590
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_020745.4(AARS2):c.149T>G(p.Phe50Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_020745.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AARS2 | NM_020745.4 | c.149T>G | p.Phe50Cys | missense_variant | 1/22 | ENST00000244571.5 | |
LOC124901322 | XR_007059594.1 | n.301-976A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AARS2 | ENST00000244571.5 | c.149T>G | p.Phe50Cys | missense_variant | 1/22 | 1 | NM_020745.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460620Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 726596
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
Leukoencephalopathy, progressive, with ovarian failure Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 10, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at