chr1-7961859-C-G
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007262.5(PARK7):c.-24+66C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 113,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PARK7
NM_007262.5 intron
NM_007262.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.269
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 Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.-24+66C>G | intron_variant | ENST00000338639.10 | NP_009193.2 | |||
PARK7 | XM_005263424.4 | c.-246C>G | 5_prime_UTR_variant | 1/7 | XP_005263481.1 | |||
PARK7 | NM_001123377.2 | c.-24+124C>G | intron_variant | NP_001116849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.-24+66C>G | intron_variant | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000106 AC: 12AN: 113410Hom.: 0 Cov.: 30
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 330Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 220
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GnomAD4 genome AF: 0.000106 AC: 12AN: 113538Hom.: 0 Cov.: 30 AF XY: 0.0000725 AC XY: 4AN XY: 55188
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
PARK7-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 13, 2024 | The PARK7 c.-24+66C>G variant is located in the 5' untranslated region. This variant, also referred to as DJ-1 g.159C>G in the literature, has been reported in an individual with early onset Parkinson disease and was shown to segregate with disease in the family (Tarantino et al. 2009. PubMed ID: 18722801). This variant is reported in 0.0065% of alleles in individuals of European (non-Finnish) descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at