chr2-222571939-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005687.5(FARSB):c.1702G>A(p.Val568Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,598 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 Uncertain significance (★).
Frequency
Consequence
NM_005687.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FARSB | NM_005687.5 | c.1702G>A | p.Val568Ile | missense_variant | Exon 17 of 17 | ENST00000281828.8 | NP_005678.3 | |
FARSB | XM_006712169.3 | c.1405G>A | p.Val469Ile | missense_variant | Exon 18 of 18 | XP_006712232.1 | ||
FARSB | XM_011510466.3 | c.1405G>A | p.Val469Ile | missense_variant | Exon 18 of 18 | XP_011508768.1 | ||
FARSB | NR_130154.2 | n.1917G>A | non_coding_transcript_exon_variant | Exon 18 of 18 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151944Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251134Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135732
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461654Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727134
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151944Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74172
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 568 of the FARSB protein (p.Val568Ile). This variant is present in population databases (rs747770664, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with FARSB-related conditions. ClinVar contains an entry for this variant (Variation ID: 1931812). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt FARSB protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at