Variant chr1-7962111-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_007262.5(PARK7):c.-24+318C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,486 control chromosomes in the GnomAD database, including 7,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 7739 hom., cov: 32)

Exomes 𝑓: 0.33 ( 28 hom. )

Consequence

PARK7
NM_007262.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.170

Variant links:

Genes affected

PARK7 (HGNC:16369): (Parkinsonism associated deglycase) The product of this gene belongs to the peptidase C56 family of proteins. It acts as a positive regulator of androgen receptor-dependent transcription. It may also function as a redox-sensitive chaperone, as a sensor for oxidative stress, and it apparently protects neurons against oxidative stress and cell death. Defects in this gene are the cause of autosomal recessive early-onset Parkinson disease 7. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008]

PARK7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 1-7962111-C-T is Benign according to our data. Variant chr1-7962111-C-T is described in ClinVar as [Benign]. Clinvar id is 1233736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
PARK7	NM_007262.5 linkuse as main transcript	c.-24+318C>T	intron_variant	ENST00000338639.10	NP_009193.2
PARK7	NM_001123377.2 linkuse as main transcript	c.-24+376C>T	intron_variant		NP_001116849.1
PARK7	XM_005263424.4 linkuse as main transcript	c.-24+30C>T	intron_variant		XP_005263481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10 linkuse as main transcript	c.-24+318C>T		intron_variant		1	NM_007262.5	ENSP00000340278	P1

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42117

AN:

151948

Hom.:

7737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0717

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.261

Gnomad ASJ

AF:

0.425

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.237

Gnomad FIN

AF:

0.334

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.409

Gnomad OTH

AF:

0.301

GnomAD4 exome

AF:

0.333

AC:

140

AN:

420

Hom.:

Cov.:

AF XY:

0.343

AC XY:

AN XY:

286

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0714

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.273

Gnomad4 FIN exome

AF:

0.333

Gnomad4 NFE exome

AF:

0.386

Gnomad4 OTH exome

AF:

0.333

GnomAD4 genome

AF:

0.277

AC:

42110

AN:

152066

Hom.:

7739

Cov.:

AF XY:

0.272

AC XY:

20184

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.0715

Gnomad4 AMR

AF:

0.261

Gnomad4 ASJ

AF:

0.425

Gnomad4 EAS

AF:

0.00270

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.334

Gnomad4 NFE

AF:

0.409

Gnomad4 OTH

AF:

0.296

Alfa

AF:

0.146

Hom.:

334

Bravo

AF:

0.262

Asia WGS

AF:

0.114

AC:

395

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 15, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.7

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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