1-20633737-C-T

Position:

chr1-20633737-C-T

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_032409.3(PINK1):c.189C>T(p.Leu63=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 1,537,436 control chromosomes in the GnomAD database, including 28,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.16 ( 2121 hom., cov: 32)

Exomes 𝑓: 0.19 ( 25996 hom. )

Consequence

PINK1
NM_032409.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:10

Conservation

PhyloP100: -1.15

Variant links:

Genes affected

PINK1 (HGNC:14581): (PTEN induced kinase 1) This gene encodes a serine/threonine protein kinase that localizes to mitochondria. It is thought to protect cells from stress-induced mitochondrial dysfunction. Mutations in this gene cause one form of autosomal recessive early-onset Parkinson disease. [provided by RefSeq, Jul 2008]

PINK1 links:

MIR6084 (HGNC:50235): (microRNA 6084) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

MIR6084 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BP6

Variant 1-20633737-C-T is Benign according to our data. Variant chr1-20633737-C-T is described in ClinVar as [Benign]. Clinvar id is 262026.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-20633737-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PINK1	NM_032409.3 linkuse as main transcript	c.189C>T	p.Leu63=	synonymous_variant	1/8	ENST00000321556.5	NP_115785.1
MIR6084	NR_106732.1 linkuse as main transcript	n.59C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PINK1	ENST00000321556.5 linkuse as main transcript	c.189C>T	p.Leu63=	synonymous_variant	1/8	1	NM_032409.3	ENSP00000364204	P1	Q9BXM7-1
MIR6084	ENST00000622012.1 linkuse as main transcript	n.59C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23658

AN:

151890

Hom.:

2119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0662

Gnomad AMI

AF:

0.198

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.140

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.248

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.186

GnomAD3 exomes

AF:

0.176

AC:

23446

AN:

133556

Hom.:

2227

AF XY:

0.178

AC XY:

13042

AN XY:

73426

show subpopulations

Gnomad AFR exome

AF:

0.0662

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.270

Gnomad EAS exome

AF:

0.149

Gnomad SAS exome

AF:

0.154

Gnomad FIN exome

AF:

0.179

Gnomad NFE exome

AF:

0.200

Gnomad OTH exome

AF:

0.201

GnomAD4 exome

AF:

0.190

AC:

263229

AN:

1385438

Hom.:

25996

Cov.:

AF XY:

0.190

AC XY:

129910

AN XY:

684130

show subpopulations

Gnomad4 AFR exome

AF:

0.0650

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.265

Gnomad4 EAS exome

AF:

0.131

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.181

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.186

GnomAD4 genome

AF:

0.156

AC:

23651

AN:

151998

Hom.:

2121

Cov.:

AF XY:

0.153

AC XY:

11393

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.0660

Gnomad4 AMR

AF:

0.145

Gnomad4 ASJ

AF:

0.267

Gnomad4 EAS

AF:

0.140

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.185

Alfa

AF:

0.192

Hom.:

704

Bravo

AF:

0.151

Asia WGS

AF:

0.134

AC:

464

AN:

3458

ClinVar

Significance: Benign

Submissions summary: Benign:10

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan	Jul 31, 2024	This variant is classified as Benign based on local population frequency. This variant was detected in 24% 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: 22. Only high quality variants are reported. -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 01, 2017	- -

Autosomal recessive early-onset Parkinson disease 6

Benign:3

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 27, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

DANN

Benign

0.89

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