1-7969450-G-T
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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.252+46G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000945 in 740,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000014 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000084 ( 0 hom. )
Consequence
PARK7
NM_007262.5 intron
NM_007262.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.75
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=-0.83).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.252+46G>T | intron_variant | ENST00000338639.10 | NP_009193.2 | |||
PARK7 | NM_001123377.2 | c.252+46G>T | intron_variant | NP_001116849.1 | ||||
PARK7 | XM_005263424.4 | c.252+46G>T | intron_variant | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.252+46G>T | intron_variant | 1 | NM_007262.5 | ENSP00000340278.5 |
Frequencies
GnomAD3 genomes AF: 0.0000139 AC: 2AN: 143410Hom.: 0 Cov.: 29
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GnomAD4 exome AF: 0.00000837 AC: 5AN: 597132Hom.: 0 Cov.: 10 AF XY: 0.00000625 AC XY: 2AN XY: 319926
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GnomAD4 genome AF: 0.0000139 AC: 2AN: 143410Hom.: 0 Cov.: 29 AF XY: 0.0000289 AC XY: 2AN XY: 69232
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ClinVar
Not reported inComputational 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