1-7962740-CTTTTTTTT-CTT
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_007262.5(PARK7):c.-23-9_-23-4delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,153,652 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000087 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000087 ( 0 hom. )
Consequence
PARK7
NM_007262.5 splice_region, intron
NM_007262.5 splice_region, intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.11
Genes affected
PARK7 (HGNC:16369): (Parkinsonism associated deglycase) The product of this gene belongs to the peptidase C56 family of proteins. It acts as a positive regulator of androgen receptor-dependent transcription. It may also function as a redox-sensitive chaperone, as a sensor for oxidative stress, and it apparently protects neurons against oxidative stress and cell death. Defects in this gene are the cause of autosomal recessive early-onset Parkinson disease 7. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.-23-9_-23-4delTTTTTT | splice_region_variant, intron_variant | Intron 1 of 6 | ENST00000338639.10 | NP_009193.2 | ||
PARK7 | NM_001123377.2 | c.-23-9_-23-4delTTTTTT | splice_region_variant, intron_variant | Intron 1 of 6 | NP_001116849.1 | |||
PARK7 | XM_005263424.4 | c.-23-9_-23-4delTTTTTT | splice_region_variant, intron_variant | Intron 1 of 6 | XP_005263481.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000868 AC: 1AN: 115208Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000867 AC: 9AN: 1038444Hom.: 0 AF XY: 0.00000951 AC XY: 5AN XY: 525734
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GnomAD4 genome AF: 0.00000868 AC: 1AN: 115208Hom.: 0 Cov.: 29 AF XY: 0.0000181 AC XY: 1AN XY: 55140
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at