rs41302853
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006567.5(FARS2):c.339C>T(p.Tyr113=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00933 in 1,614,142 control chromosomes in the GnomAD database, including 241 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.024 ( 93 hom., cov: 32)
Exomes 𝑓: 0.0077 ( 148 hom. )
Consequence
FARS2
NM_006567.5 synonymous
NM_006567.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.72
Genes affected
FARS2 (HGNC:21062): (phenylalanyl-tRNA synthetase 2, mitochondrial) This gene encodes a protein that transfers phenylalanine to its cognate tRNA. This protein localizes to the mitochondrion and plays a role in mitochondrial protein translation. Mutations in this gene can cause combined oxidative phosphorylation deficiency 14 (Alpers encephalopathy). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
?
Variant 6-5368909-C-T is Benign according to our data. Variant chr6-5368909-C-T is described in ClinVar as [Benign]. Clinvar id is 137289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.72 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0679 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.339C>T | p.Tyr113= | synonymous_variant | 2/7 | ENST00000274680.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.339C>T | p.Tyr113= | synonymous_variant | 2/7 | 1 | NM_006567.5 | P1 | |
FARS2 | ENST00000324331.10 | c.339C>T | p.Tyr113= | synonymous_variant | 2/7 | 1 | P1 | ||
FARS2 | ENST00000648580.1 | c.339C>T | p.Tyr113= | synonymous_variant, NMD_transcript_variant | 2/9 |
Frequencies
GnomAD3 genomes ? AF: 0.0244 AC: 3714AN: 152140Hom.: 93 Cov.: 32
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GnomAD3 exomes AF: 0.0102 AC: 2565AN: 251278Hom.: 55 AF XY: 0.00863 AC XY: 1172AN XY: 135838
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GnomAD4 exome AF: 0.00775 AC: 11328AN: 1461884Hom.: 148 Cov.: 32 AF XY: 0.00735 AC XY: 5347AN XY: 727244
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GnomAD4 genome ? AF: 0.0245 AC: 3727AN: 152258Hom.: 93 Cov.: 32 AF XY: 0.0239 AC XY: 1777AN XY: 74434
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 26, 2013 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Combined oxidative phosphorylation defect type 14 Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jun 13, 2018 | - - |
not provided Benign:1
Benign, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jan 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at