rs201991648
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_006567.5(FARS2):c.676C>T(p.His226Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000775 in 1,612,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006567.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FARS2 | NM_006567.5 | c.676C>T | p.His226Tyr | missense_variant | 3/7 | ENST00000274680.9 | NP_006558.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FARS2 | ENST00000274680.9 | c.676C>T | p.His226Tyr | missense_variant | 3/7 | 1 | NM_006567.5 | ENSP00000274680 | P1 | |
FARS2 | ENST00000324331.10 | c.676C>T | p.His226Tyr | missense_variant | 3/7 | 1 | ENSP00000316335 | P1 | ||
FARS2 | ENST00000445533.1 | c.64C>T | p.His22Tyr | missense_variant | 1/3 | 3 | ENSP00000392525 | |||
FARS2 | ENST00000648580.1 | c.676C>T | p.His226Tyr | missense_variant, NMD_transcript_variant | 3/9 | ENSP00000497889 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000423 AC: 106AN: 250738Hom.: 0 AF XY: 0.000310 AC XY: 42AN XY: 135532
GnomAD4 exome AF: 0.0000808 AC: 118AN: 1460450Hom.: 0 Cov.: 31 AF XY: 0.0000716 AC XY: 52AN XY: 726508
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
Combined oxidative phosphorylation defect type 14 Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine | Jun 13, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | - - |
FARS2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2022 | 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