GeneBe

rs193922938

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000144.5(FXN):​c.165+1343_165+1357delGAAGAAGAAGAAGAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

FXN
NM_000144.5 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.327

Publications

0 publications found
Variant links:
Genes affected
FXN (HGNC:3951): (frataxin) This nuclear gene encodes a mitochondrial protein which belongs to the FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA from 8-33 repeats to >90 repeats results in Friedreich ataxia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
FXN Gene-Disease associations (from GenCC):
  • Friedreich ataxia
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • Friedreich ataxia 1
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
  • Friedreich ataxia
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FXNNM_000144.5 linkc.165+1343_165+1357delGAAGAAGAAGAAGAA intron_variant Intron 1 of 4 ENST00000484259.3 NP_000135.2 Q16595-1A0A0S2Z3G4
FXNNM_181425.3 linkc.165+1343_165+1357delGAAGAAGAAGAAGAA intron_variant Intron 1 of 4 NP_852090.1 Q16595-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FXNENST00000484259.3 linkc.165+1338_165+1352delAAGAAGAAGAAGAAG intron_variant Intron 1 of 4 3 NM_000144.5 ENSP00000419243.2 Q16595-1
ENSG00000285130ENST00000642889.1 linkc.165+1338_165+1352delAAGAAGAAGAAGAAG intron_variant Intron 1 of 24 ENSP00000493780.1 A0A2R8YDH4

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
0.33

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs193922938; hg19: chr9-71652200; API