rs1043424
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_032409.3(PINK1):c.1562A>C(p.Asn521Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,613,924 control chromosomes in the GnomAD database, including 66,988 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_032409.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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PINK1 | ENST00000321556.5 | c.1562A>C | p.Asn521Thr | missense_variant | Exon 8 of 8 | 1 | NM_032409.3 | ENSP00000364204.3 | ||
PINK1 | ENST00000400490.2 | n.655A>C | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 | |||||
PINK1-AS | ENST00000451424.1 | n.1687T>G | non_coding_transcript_exon_variant | Exon 1 of 3 | 2 | |||||
PINK1 | ENST00000492302.1 | n.3012A>C | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.277 AC: 42053AN: 151968Hom.: 5986 Cov.: 33
GnomAD3 exomes AF: 0.292 AC: 73476AN: 251378Hom.: 11210 AF XY: 0.298 AC XY: 40462AN XY: 135876
GnomAD4 exome AF: 0.286 AC: 417477AN: 1461838Hom.: 60999 Cov.: 57 AF XY: 0.288 AC XY: 209526AN XY: 727232
GnomAD4 genome AF: 0.277 AC: 42073AN: 152086Hom.: 5989 Cov.: 33 AF XY: 0.280 AC XY: 20830AN XY: 74344
ClinVar
Submissions by phenotype
not specified Benign:6
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This variant is classified as Benign based on local population frequency. This variant was detected in 49% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy, Progressive Myoclonus Epilepsy and Abnormal Movements and Neurodegeneration with brain iron accumulation. Number of patients: 46. Only high quality variants are reported. -
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Autosomal recessive early-onset Parkinson disease 6 Benign:4
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
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not provided Benign:2
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This variant is associated with the following publications: (PMID: 31182772, 30917570, 21677397, 23303188, 23459931) -
Congenital disorder of glycosylation Benign:1
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Parkinson Disease, Recessive Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at