rs201927340
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006567.5(FARS2):āc.781A>Gā(p.Ile261Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,613,556 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I261L) has been classified as Uncertain significance.
Frequency
Consequence
NM_006567.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.781A>G | p.Ile261Val | missense_variant | 4/7 | ENST00000274680.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.781A>G | p.Ile261Val | missense_variant | 4/7 | 1 | NM_006567.5 | P1 | |
FARS2 | ENST00000324331.10 | c.781A>G | p.Ile261Val | missense_variant | 4/7 | 1 | P1 | ||
FARS2 | ENST00000445533.1 | c.169A>G | p.Ile57Val | missense_variant | 2/3 | 3 | |||
FARS2 | ENST00000648580.1 | c.781A>G | p.Ile261Val | missense_variant, NMD_transcript_variant | 4/9 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 251094Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135702
GnomAD4 exome AF: 0.0000493 AC: 72AN: 1461222Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 34AN XY: 726876
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74498
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at