rs6937817

Variant summary

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

The ENST00000366898.6(PRKN):​c.1083+52549A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,158 control chromosomes in the GnomAD database, including 22,425 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 0.52 ( 22425 hom., cov: 33)

Consequence

PRKN
ENST00000366898.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.205
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=-1.02).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PRKNNM_004562.3 linkuse as main transcriptc.1083+52549A>G intron_variant ENST00000366898.6 NP_004553.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PRKNENST00000366898.6 linkuse as main transcriptc.1083+52549A>G intron_variant 1 NM_004562.3 ENSP00000355865 P1O60260-1

Frequencies

GnomAD3 genomes
AF:
0.516
AC:
78409
AN:
152040
Hom.:
22384
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.765
Gnomad AMI
AF:
0.364
Gnomad AMR
AF:
0.411
Gnomad ASJ
AF:
0.476
Gnomad EAS
AF:
0.156
Gnomad SAS
AF:
0.293
Gnomad FIN
AF:
0.388
Gnomad MID
AF:
0.484
Gnomad NFE
AF:
0.455
Gnomad OTH
AF:
0.498
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.516
AC:
78504
AN:
152158
Hom.:
22425
Cov.:
33
AF XY:
0.505
AC XY:
37561
AN XY:
74388
show subpopulations
Gnomad4 AFR
AF:
0.765
Gnomad4 AMR
AF:
0.410
Gnomad4 ASJ
AF:
0.476
Gnomad4 EAS
AF:
0.156
Gnomad4 SAS
AF:
0.292
Gnomad4 FIN
AF:
0.388
Gnomad4 NFE
AF:
0.455
Gnomad4 OTH
AF:
0.498
Alfa
AF:
0.382
Hom.:
1598
Bravo
AF:
0.531
Asia WGS
AF:
0.277
AC:
964
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.6
DANN
Benign
0.46

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: rs6937817; hg19: chr6-161917337; COSMIC: COSV58264964; API