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rs9364628

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004562.3(PRKN):c.734+55048A>G variant causes a intron change. The variant allele was found at a frequency of 0.473 in 152,000 control chromosomes in the GnomAD database, including 17,684 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 0.47 ( 17684 hom., cov: 32)

Consequence

PRKN
NM_004562.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.77
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PRKNNM_004562.3 linkuse as main transcriptc.734+55048A>G intron_variant ENST00000366898.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PRKNENST00000366898.6 linkuse as main transcriptc.734+55048A>G intron_variant 1 NM_004562.3 P1O60260-1

Frequencies

GnomAD3 genomes
AF:
0.473
AC:
71808
AN:
151882
Hom.:
17651
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.602
Gnomad AMI
AF:
0.475
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.492
Gnomad EAS
AF:
0.213
Gnomad SAS
AF:
0.356
Gnomad FIN
AF:
0.451
Gnomad MID
AF:
0.617
Gnomad NFE
AF:
0.438
Gnomad OTH
AF:
0.466
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.473
AC:
71888
AN:
152000
Hom.:
17684
Cov.:
32
AF XY:
0.471
AC XY:
34958
AN XY:
74282
show subpopulations
Gnomad4 AFR
AF:
0.602
Gnomad4 AMR
AF:
0.411
Gnomad4 ASJ
AF:
0.492
Gnomad4 EAS
AF:
0.213
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.451
Gnomad4 NFE
AF:
0.438
Gnomad4 OTH
AF:
0.462
Alfa
AF:
0.443
Hom.:
31008
Bravo
AF:
0.473
Asia WGS
AF:
0.315
AC:
1094
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.59
Cadd
Benign
11
Dann
Benign
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9364628; hg19: chr6-162339286; API