chr1-7961850-GGTGCTGGACGGTGTCCCT-G
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_007262.5(PARK7):c.-24+75_-24+92del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,158 control chromosomes in the GnomAD database, including 1,911 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 1911 hom., cov: 30)
Exomes 𝑓: 0.026 ( 0 hom. )
Consequence
PARK7
NM_007262.5 intron
NM_007262.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.721
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 Benign. Variant got -10 ACMG points.
BP6
Variant 1-7961850-GGTGCTGGACGGTGTCCCT-G is Benign according to our data. Variant chr1-7961850-GGTGCTGGACGGTGTCCCT-G is described in ClinVar as [Benign]. Clinvar id is 1246972.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.-24+75_-24+92del | intron_variant | ENST00000338639.10 | NP_009193.2 | |||
PARK7 | XM_005263424.4 | c.-237_-220del | 5_prime_UTR_variant | 1/7 | XP_005263481.1 | |||
PARK7 | NM_001123377.2 | c.-24+133_-24+150del | intron_variant | NP_001116849.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.-24+75_-24+92del | intron_variant | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.140 AC: 21183AN: 151770Hom.: 1909 Cov.: 30
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GnomAD4 exome AF: 0.0257 AC: 7AN: 272Hom.: 0 AF XY: 0.0275 AC XY: 5AN XY: 182
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GnomAD4 genome AF: 0.139 AC: 21179AN: 151886Hom.: 1911 Cov.: 30 AF XY: 0.142 AC XY: 10547AN XY: 74220
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 04, 2019 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at