rs951916099
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_006567.5(FARS2):c.750C>A(p.Leu250=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000438 in 1,598,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L250L) has been classified as Likely benign.
Frequency
Consequence
NM_006567.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.750C>A | p.Leu250= | synonymous_variant | 3/7 | ENST00000274680.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.750C>A | p.Leu250= | synonymous_variant | 3/7 | 1 | NM_006567.5 | P1 | |
FARS2 | ENST00000324331.10 | c.750C>A | p.Leu250= | synonymous_variant | 3/7 | 1 | P1 | ||
FARS2 | ENST00000445533.1 | c.138C>A | p.Leu46= | synonymous_variant | 1/3 | 3 | |||
FARS2 | ENST00000648580.1 | c.750C>A | p.Leu250= | synonymous_variant, NMD_transcript_variant | 3/9 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151644Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000407 AC: 1AN: 245800Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132852
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1446580Hom.: 0 Cov.: 31 AF XY: 0.00000417 AC XY: 3AN XY: 719004
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151644Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73972
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at