6-161815043-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004562.3(PRKN):c.735-29135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,158 control chromosomes in the GnomAD database, including 61,459 homozygotes. 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 0.90 ( 61459 hom., cov: 31)
Consequence
PRKN
NM_004562.3 intron
NM_004562.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0110
Publications
15 publications found
Genes affected
PRKN (HGNC:8607): (parkin RBR E3 ubiquitin protein ligase) The precise function of this gene is unknown; however, the encoded protein is a component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrate proteins for proteasomal degradation. Mutations in this gene are known to cause Parkinson disease and autosomal recessive juvenile Parkinson disease. Alternative splicing of this gene produces multiple transcript variants encoding distinct isoforms. Additional splice variants of this gene have been described but currently lack transcript support. [provided by RefSeq, Jul 2008]
PRKN Gene-Disease associations (from GenCC):
- autosomal recessive juvenile Parkinson disease 2Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Laboratory for Molecular Medicine, Genomics England PanelApp
- Parkinson diseaseInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- young-onset Parkinson diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.898 AC: 136558AN: 152040Hom.: 61427 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
136558
AN:
152040
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.898 AC: 136642AN: 152158Hom.: 61459 Cov.: 31 AF XY: 0.894 AC XY: 66506AN XY: 74376 show subpopulations
GnomAD4 genome
AF:
AC:
136642
AN:
152158
Hom.:
Cov.:
31
AF XY:
AC XY:
66506
AN XY:
74376
show subpopulations
African (AFR)
AF:
AC:
38297
AN:
41532
American (AMR)
AF:
AC:
14109
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
3019
AN:
3470
East Asian (EAS)
AF:
AC:
4604
AN:
5158
South Asian (SAS)
AF:
AC:
3747
AN:
4808
European-Finnish (FIN)
AF:
AC:
9147
AN:
10580
Middle Eastern (MID)
AF:
AC:
237
AN:
292
European-Non Finnish (NFE)
AF:
AC:
60865
AN:
68014
Other (OTH)
AF:
AC:
1857
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.505
Heterozygous variant carriers
0
726
1452
2179
2905
3631
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
904
1808
2712
3616
4520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2834
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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