Variant chr1-7969434-T-G 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.252+30T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 910,904 control chromosomes in the GnomAD database, including 39,439 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 4959 hom., cov: 31)

Exomes 𝑓: 0.34 ( 34480 hom. )

Consequence

PARK7
NM_007262.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.194

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:

PARK7 (HGNC:):

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=-0.89).

BP6

Variant 1-7969434-T-G is Benign according to our data. Variant chr1-7969434-T-G is described in ClinVar as [Benign]. Clinvar id is 1227164.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-7969434-T-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PARK7	NM_007262.5 linkuse as main transcript	c.252+30T>G	intron_variant	ENST00000338639.10	NP_009193.2	Q99497V9HWC2
PARK7	NM_001123377.2 linkuse as main transcript	c.252+30T>G	intron_variant		NP_001116849.1	Q99497V9HWC2
PARK7	XM_005263424.4 linkuse as main transcript	c.252+30T>G	intron_variant		XP_005263481.1	Q99497V9HWC2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10 linkuse as main transcript	c.252+30T>G		intron_variant		1	NM_007262.5	ENSP00000340278.5		Q99497

Frequencies

GnomAD3 genomes

AF:

0.256

AC:

35203

AN:

137702

Hom.:

4948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.316

Gnomad AMI

AF:

0.0674

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.653

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.0935

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.220

GnomAD3 exomes

AF:

0.264

AC:

61778

AN:

233574

Hom.:

11104

AF XY:

0.243

AC XY:

30732

AN XY:

126668

show subpopulations

Gnomad AFR exome

AF:

0.305

Gnomad AMR exome

AF:

0.486

Gnomad ASJ exome

AF:

0.0894

Gnomad EAS exome

AF:

0.641

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.296

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

AF:

0.336

AC:

259416

AN:

773052

Hom.:

34480

Cov.:

AF XY:

0.315

AC XY:

126405

AN XY:

401878

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.495

Gnomad4 ASJ exome

AF:

0.140

Gnomad4 EAS exome

AF:

0.673

Gnomad4 SAS exome

AF:

0.131

Gnomad4 FIN exome

AF:

0.349

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.330

GnomAD4 genome

AF:

0.256

AC:

35252

AN:

137852

Hom.:

4959

Cov.:

AF XY:

0.266

AC XY:

17764

AN XY:

66716

show subpopulations

Gnomad4 AFR

AF:

0.316

Gnomad4 AMR

AF:

0.352

Gnomad4 ASJ

AF:

0.0922

Gnomad4 EAS

AF:

0.653

Gnomad4 SAS

AF:

0.156

Gnomad4 FIN

AF:

0.341

Gnomad4 NFE

AF:

0.177

Gnomad4 OTH

AF:

0.220

Alfa

AF:

0.129

Hom.:

372

Bravo

AF:

0.246

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.36

DANN

Benign

0.71

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