chr9-69035879-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000144.5(FXN):āc.97T>Gā(p.Leu33Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000156 in 1,469,842 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Synonymous variant affecting the same amino acid position (i.e. L33L) has been classified as Likely benign.
Frequency
Consequence
NM_000144.5 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 |
---|---|---|---|---|---|---|---|
FXN | NM_000144.5 | c.97T>G | p.Leu33Val | missense_variant | 1/5 | ENST00000484259.3 | |
FXN | NM_181425.3 | c.97T>G | p.Leu33Val | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FXN | ENST00000484259.3 | c.97T>G | p.Leu33Val | missense_variant | 1/5 | 3 | NM_000144.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000134 AC: 2AN: 149750Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000314 AC: 3AN: 95482Hom.: 0 AF XY: 0.0000374 AC XY: 2AN XY: 53530
GnomAD4 exome AF: 0.0000159 AC: 21AN: 1319974Hom.: 1 Cov.: 36 AF XY: 0.0000138 AC XY: 9AN XY: 651138
GnomAD4 genome AF: 0.0000133 AC: 2AN: 149868Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 73208
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 02, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at