1-7962839-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007262.5(PARK7):c.54G>A(p.Glu18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,612,576 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 Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
PARK7
NM_007262.5 synonymous
NM_007262.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.71
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 1-7962839-G-A is Benign according to our data. Variant chr1-7962839-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2038134.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.71 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.54G>A | p.Glu18= | synonymous_variant | 2/7 | ENST00000338639.10 | NP_009193.2 | |
PARK7 | NM_001123377.2 | c.54G>A | p.Glu18= | synonymous_variant | 2/7 | NP_001116849.1 | ||
PARK7 | XM_005263424.4 | c.54G>A | p.Glu18= | synonymous_variant | 2/7 | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.54G>A | p.Glu18= | synonymous_variant | 2/7 | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000663 AC: 1AN: 150858Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251486Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135920
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461718Hom.: 0 Cov.: 33 AF XY: 0.00000550 AC XY: 4AN XY: 727166
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GnomAD4 genome AF: 0.00000663 AC: 1AN: 150858Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1AN XY: 73512
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive early-onset Parkinson disease 7 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 09, 2022 | - - |
Computational scores
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Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at