chr2-222571888-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005687.5(FARSB):c.1753G>A(p.Val585Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 1,612,028 control chromosomes in the GnomAD database, including 609,470 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005687.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARSB | NM_005687.5 | c.1753G>A | p.Val585Ile | missense_variant | 17/17 | ENST00000281828.8 | |
FARSB | XM_006712169.3 | c.1456G>A | p.Val486Ile | missense_variant | 18/18 | ||
FARSB | XM_011510466.3 | c.1456G>A | p.Val486Ile | missense_variant | 18/18 | ||
FARSB | NR_130154.2 | n.1968G>A | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARSB | ENST00000281828.8 | c.1753G>A | p.Val585Ile | missense_variant | 17/17 | 1 | NM_005687.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.830 AC: 125898AN: 151740Hom.: 52984 Cov.: 28
GnomAD3 exomes AF: 0.885 AC: 221251AN: 249936Hom.: 98453 AF XY: 0.889 AC XY: 120124AN XY: 135078
GnomAD4 exome AF: 0.872 AC: 1273160AN: 1460170Hom.: 556453 Cov.: 39 AF XY: 0.874 AC XY: 634961AN XY: 726436
GnomAD4 genome ? AF: 0.830 AC: 125980AN: 151858Hom.: 53017 Cov.: 28 AF XY: 0.835 AC XY: 61993AN XY: 74226
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
FARSB-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as 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