9-69072677-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_000144.5(FXN):c.548A>T(p.His183Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,890 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.
Frequency
Consequence
NM_000144.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FXN | NM_000144.5 | c.548A>T | p.His183Leu | missense_variant | Exon 5 of 5 | ENST00000484259.3 | NP_000135.2 | |
FXN | NM_181425.3 | c.556A>T | p.Met186Leu | missense_variant | Exon 5 of 5 | NP_852090.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FXN | ENST00000484259.3 | c.548A>T | p.His183Leu | missense_variant | Exon 5 of 5 | 3 | NM_000144.5 | ENSP00000419243.2 | ||
ENSG00000285130 | ENST00000642889.1 | c.166-27224A>T | intron_variant | Intron 1 of 24 | ENSP00000493780.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461890Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0AN XY: 727244
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at