rs150477330
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_006567.5(FARS2):c.462G>A(p.Ala154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000132 in 1,613,984 control chromosomes in the GnomAD database, including 2 homozygotes. 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. A154A) has been classified as Likely benign.
Frequency
Consequence
NM_006567.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.462G>A | p.Ala154= | synonymous_variant | 2/7 | ENST00000274680.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.462G>A | p.Ala154= | synonymous_variant | 2/7 | 1 | NM_006567.5 | P1 | |
FARS2 | ENST00000324331.10 | c.462G>A | p.Ala154= | synonymous_variant | 2/7 | 1 | P1 | ||
FARS2 | ENST00000648580.1 | c.462G>A | p.Ala154= | synonymous_variant, NMD_transcript_variant | 2/9 |
Frequencies
GnomAD3 genomes ? AF: 0.0000658 AC: 10AN: 152042Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000255 AC: 64AN: 251254Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135842
GnomAD4 exome AF: 0.000139 AC: 203AN: 1461824Hom.: 1 Cov.: 32 AF XY: 0.000198 AC XY: 144AN XY: 727216
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152160Hom.: 1 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74406
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 19, 2024 | - - |
FARS2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at