Variant 1-7982766-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007262.5(PARK7):c.410-2128G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,090 control chromosomes in the GnomAD database, including 5,656 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.25 ( 5656 hom., cov: 32)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

PARK7
NM_007262.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0860

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 -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
PARK7	NM_007262.5 linkuse as main transcript	c.410-2128G>T	intron_variant	ENST00000338639.10
PARK7	NM_001123377.2 linkuse as main transcript	c.410-2128G>T	intron_variant
PARK7	XM_005263424.4 linkuse as main transcript	c.410-2128G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARK7	ENST00000338639.10 linkuse as main transcript	c.410-2128G>T		intron_variant		1	NM_007262.5	P1

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

38016

AN:

151964

Hom.:

5646

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.0746

Gnomad AMR

AF:

0.347

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.629

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.219

GnomAD4 exome

AF:

0.125

AC:

AN:

Hom.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.250

AC:

38063

AN:

152082

Hom.:

5656

Cov.:

AF XY:

0.256

AC XY:

19045

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.312

Gnomad4 AMR

AF:

0.348

Gnomad4 ASJ

AF:

0.121

Gnomad4 EAS

AF:

0.628

Gnomad4 SAS

AF:

0.134

Gnomad4 FIN

AF:

0.293

Gnomad4 NFE

AF:

0.174

Gnomad4 OTH

AF:

0.219

Alfa

AF:

0.177

Hom.:

3093

Bravo

AF:

0.266

Asia WGS

AF:

0.373

AC:

1296

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

9.6

DANN

Benign

0.61

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over