1-7962740-CTT-C
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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.-23-5_-23-4del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 1,107,842 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00053 ( 0 hom., cov: 29)
Exomes 𝑓: 0.037 ( 0 hom. )
Consequence
PARK7
NM_007262.5 intron
NM_007262.5 intron
Scores
Not classified
Clinical Significance
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 Benign. Variant got -10 ACMG points.
BP6
Variant 1-7962740-CTT-C is Benign according to our data. Variant chr1-7962740-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1229912.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.-23-5_-23-4del | intron_variant | ENST00000338639.10 | NP_009193.2 | |||
PARK7 | NM_001123377.2 | c.-23-5_-23-4del | intron_variant | NP_001116849.1 | ||||
PARK7 | XM_005263424.4 | c.-23-5_-23-4del | intron_variant | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.-23-5_-23-4del | intron_variant | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000530 AC: 61AN: 115110Hom.: 0 Cov.: 29
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GnomAD3 exomes AF: 0.0481 AC: 4325AN: 89970Hom.: 0 AF XY: 0.0486 AC XY: 2400AN XY: 49406
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GnomAD4 exome AF: 0.0372 AC: 36939AN: 992744Hom.: 0 AF XY: 0.0365 AC XY: 18333AN XY: 502248
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GnomAD4 genome AF: 0.000530 AC: 61AN: 115098Hom.: 0 Cov.: 29 AF XY: 0.000526 AC XY: 29AN XY: 55106
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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 | May 23, 2021 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at