Variant chr1-7961913-G-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+120G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,330 control chromosomes in the GnomAD database, including 2,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.18 ( 2900 hom., cov: 33)

Exomes 𝑓: 0.13 ( 1 hom. )

Consequence

PARK7
NM_007262.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.226

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=-0.88).

BP6

Variant 1-7961913-G-T is Benign according to our data. Variant chr1-7961913-G-T is described in ClinVar as [Benign]. Clinvar id is 1243450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
PARK7	NM_007262.5 linkuse as main transcript	c.-24+120G>T	intron_variant		ENST00000338639.10	NP_009193.2
PARK7	XM_005263424.4 linkuse as main transcript	c.-192G>T	5_prime_UTR_variant	1/7		XP_005263481.1
PARK7	NM_001123377.2 linkuse as main transcript	c.-24+178G>T	intron_variant			NP_001116849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10 linkuse as main transcript	c.-24+120G>T		intron_variant		1	NM_007262.5	ENSP00000340278	P1

Frequencies

GnomAD3 genomes

AF:

0.184

AC:

28030

AN:

152054

Hom.:

2892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.118

Gnomad ASJ

AF:

0.107

Gnomad EAS

AF:

0.0630

Gnomad SAS

AF:

0.0961

Gnomad FIN

AF:

0.287

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.131

AC:

AN:

160

Hom.:

Cov.:

AF XY:

0.136

AC XY:

AN XY:

110

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.125

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.137

Gnomad4 OTH exome

AF:

0.100

GnomAD4 genome

AF:

0.184

AC:

28061

AN:

152170

Hom.:

2900

Cov.:

AF XY:

0.184

AC XY:

13728

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.118

Gnomad4 ASJ

AF:

0.107

Gnomad4 EAS

AF:

0.0628

Gnomad4 SAS

AF:

0.0957

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.166

Gnomad4 OTH

AF:

0.159

Alfa

AF:

0.147

Hom.:

1599

Bravo

AF:

0.178

Asia WGS

AF:

0.0840

AC:

294

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 14, 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

-0.88

CADD

Benign

5.3

DANN

Benign

0.84

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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