1-7961680-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000493373.5(PARK7):c.-23-1083G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 153,500 control chromosomes in the GnomAD database, including 4,065 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.21 ( 4050 hom., cov: 33)
Exomes 𝑓: 0.13 ( 15 hom. )
Consequence
PARK7
ENST00000493373.5 intron
ENST00000493373.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.53
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 1-7961680-G-A is Benign according to our data. Variant chr1-7961680-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 298111.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | upstream_gene_variant | ENST00000338639.10 | NP_009193.2 | ||||
PARK7 | NM_001123377.2 | upstream_gene_variant | NP_001116849.1 | |||||
PARK7 | XM_005263424.4 | upstream_gene_variant | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | upstream_gene_variant | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32055AN: 152098Hom.: 4034 Cov.: 33
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GnomAD4 exome AF: 0.125 AC: 161AN: 1286Hom.: 15 Cov.: 0 AF XY: 0.125 AC XY: 120AN XY: 962
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GnomAD4 genome AF: 0.211 AC: 32105AN: 152214Hom.: 4050 Cov.: 33 AF XY: 0.210 AC XY: 15649AN XY: 74416
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 14, 2018 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Parkinson Disease, Recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at