1-20633617-C-G
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_032409.3(PINK1):āc.69C>Gā(p.Gly23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000155 in 1,290,722 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 (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 8.8e-7 ( 0 hom. )
Consequence
PINK1
NM_032409.3 synonymous
NM_032409.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.36
Genes affected
PINK1 (HGNC:14581): (PTEN induced kinase 1) This gene encodes a serine/threonine protein kinase that localizes to mitochondria. It is thought to protect cells from stress-induced mitochondrial dysfunction. Mutations in this gene cause one form of autosomal recessive early-onset Parkinson disease. [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=-0.68).
BP6
Variant 1-20633617-C-G is Benign according to our data. Variant chr1-20633617-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1602646.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.36 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| PINK1 | NM_032409.3 | c.69C>G | p.Gly23= | synonymous_variant | 1/8 | ENST00000321556.5 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PINK1 | ENST00000321556.5 | c.69C>G | p.Gly23= | synonymous_variant | 1/8 | 1 | NM_032409.3 | P1 |
Frequencies
GnomAD3 genomes 0.00000661 AC: 1AN: 151390Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 8.78e-7 AC: 1AN: 1139332Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 546480
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GnomAD4 genome 0.00000661 AC: 1AN: 151390Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73960
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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 6 Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 03, 2023 | - - |
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