chr2-222599972-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005687.5(FARSB):c.1574C>T(p.Pro525Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,609,002 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FARSB | NM_005687.5 | c.1574C>T | p.Pro525Leu | missense_variant | 16/17 | ENST00000281828.8 | |
FARSB | XM_006712169.3 | c.1277C>T | p.Pro426Leu | missense_variant | 17/18 | ||
FARSB | XM_011510466.3 | c.1277C>T | p.Pro426Leu | missense_variant | 17/18 | ||
FARSB | NR_130154.2 | n.1789C>T | non_coding_transcript_exon_variant | 17/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FARSB | ENST00000281828.8 | c.1574C>T | p.Pro525Leu | missense_variant | 16/17 | 1 | NM_005687.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152072Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000815 AC: 2AN: 245388Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132744
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456812Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 724700
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74424
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.1574C>T (p.P525L) alteration is located in exon 16 (coding exon 16) of the FARSB gene. This alteration results from a C to T substitution at nucleotide position 1574, causing the proline (P) at amino acid position 525 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at