1-20650507-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_032409.3(PINK1):c.1562A>G(p.Asn521Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N521T) has been classified as Likely benign.
Frequency
Consequence
NM_032409.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PINK1 | ENST00000321556.5 | c.1562A>G | p.Asn521Ser | missense_variant | 8/8 | 1 | NM_032409.3 | ENSP00000364204.3 | ||
PINK1 | ENST00000400490.2 | n.655A>G | non_coding_transcript_exon_variant | 4/4 | 2 | |||||
PINK1-AS | ENST00000451424.1 | n.1687T>C | non_coding_transcript_exon_variant | 1/3 | 2 | |||||
PINK1 | ENST00000492302.1 | n.3012A>G | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 57
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at