rs104894107
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP3_Strong
The NM_000144.5(FXN):āc.389G>Cā(p.Gly130Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000241 in 1,454,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G130V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000144.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FXN | NM_000144.5 | c.389G>C | p.Gly130Ala | missense_variant | 4/5 | ENST00000484259.3 | |
FXN | NM_181425.3 | c.389G>C | p.Gly130Ala | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXN | ENST00000484259.3 | c.389G>C | p.Gly130Ala | missense_variant | 4/5 | 3 | NM_000144.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251458Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135904
GnomAD4 exome AF: 0.0000241 AC: 35AN: 1454046Hom.: 0 Cov.: 29 AF XY: 0.0000359 AC XY: 26AN XY: 723994
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at