6-162262692-G-T

Position:

chr6-162262692-G-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NM_004562.3(PRKN):c.245C>A(p.Ala82Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00272 in 1,611,002 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 17 hom. )

Consequence

PRKN
NM_004562.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts P:1U:1B:3

Conservation

PhyloP100: 0.326

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]

PRKN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.12635306).

BP6

Variant 6-162262692-G-T is Benign according to our data. Variant chr6-162262692-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 7038.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAdExome4 at 17 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKN	NM_004562.3 linkuse as main transcript	c.245C>A	p.Ala82Glu	missense_variant	3/12	ENST00000366898.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKN	ENST00000366898.6 linkuse as main transcript	c.245C>A	p.Ala82Glu	missense_variant	3/12	1	NM_004562.3	P1	O60260-1

Frequencies

GnomAD3 genomes

AF:

0.00211

AC:

315

AN:

149580

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000494

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00135

Gnomad ASJ

AF:

0.00376

Gnomad EAS

AF:

0.000197

Gnomad SAS

AF:

0.00211

Gnomad FIN

AF:

0.00452

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00299

Gnomad OTH

AF:

0.00146

GnomAD3 exomes

AF:

0.00359

AC:

902

AN:

251272

Hom.:

AF XY:

0.00384

AC XY:

521

AN XY:

135840

show subpopulations

Gnomad AFR exome

AF:

0.000431

Gnomad AMR exome

AF:

0.000318

Gnomad ASJ exome

AF:

0.00456

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00183

Gnomad FIN exome

AF:

0.00615

Gnomad NFE exome

AF:

0.00541

Gnomad OTH exome

AF:

0.00570

GnomAD4 exome

AF:

0.00279

AC:

4073

AN:

1461308

Hom.:

Cov.:

AF XY:

0.00286

AC XY:

2082

AN XY:

727026

show subpopulations

Gnomad4 AFR exome

AF:

0.000418

Gnomad4 AMR exome

AF:

0.000537

Gnomad4 ASJ exome

AF:

0.00444

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00223

Gnomad4 FIN exome

AF:

0.00685

Gnomad4 NFE exome

AF:

0.00280

Gnomad4 OTH exome

AF:

0.00368

GnomAD4 genome

AF:

0.00210

AC:

314

AN:

149694

Hom.:

Cov.:

AF XY:

0.00212

AC XY:

154

AN XY:

72758

show subpopulations

Gnomad4 AFR

AF:

0.000468

Gnomad4 AMR

AF:

0.00135

Gnomad4 ASJ

AF:

0.00376

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.00211

Gnomad4 FIN

AF:

0.00452

Gnomad4 NFE

AF:

0.00300

Gnomad4 OTH

AF:

0.00145

Alfa

AF:

0.00272

Hom.:

Bravo

AF:

0.00191

TwinsUK

AF:

0.00216

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00256

AC:

ExAC

AF:

0.00474

AC:

575

Asia WGS

AF:

0.000289

AC:

AN:

3478

EpiCase

AF:

0.00294

EpiControl

AF:

0.00314

ClinVar

Significance: Benign/Likely benign

Submissions summary: Pathogenic:1Uncertain:1Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Autosomal recessive juvenile Parkinson disease 2

Pathogenic:1Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Molecular Genetics, Royal Melbourne Hospital	May 04, 2023	European Non-Finnish population allele frequency is 0.5053% (rs55774500, 902/251272 alleles, 5 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.5.1, this variant is classified as LIKELY BENIGN. Following criteria are met: BS1 -
Pathogenic, flagged submission	literature only	OMIM	Aug 01, 2001	- -

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2023	PRKN: PM5, BP4, BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 30, 2024	- -

not specified

Uncertain:1

Uncertain significance, flagged submission

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Identified in 1/344 patients with PD and in 0/340 controls. No new evidence since then. Several publications in HGMD describe it as polymorphism/ non pathogenic -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.093

BayesDel_addAF

Benign

-0.22

BayesDel_noAF

Benign

-0.090

CADD

Benign

2.9

DANN

Benign

0.36

DEOGEN2

Benign

0.11

T;.;T;T;T

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.079

LIST_S2

Benign

0.72

T;T;T;T;T

MetaRNN

Benign

0.13

T;T;T;T;T

MetaSVM

Benign

-0.81

MutationTaster

Benign

4.2e-11

A;A;A;A;A;A

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.38

N;N;N;.;.

REVEL

Uncertain

0.56

Sift

Benign

0.64

T;T;T;.;.

Sift4G

Benign

1.0

T;T;T;T;T

Polyphen

0.026

B;.;.;.;.

Vest4

0.12

MVP

0.88

MPC

0.075

ClinPred

0.0011

GERP RS

-0.77

Varity_R

0.066

gMVP

0.25

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over