chr1-7962740-CT-C

Position:

• chr1-7962740-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_007262.5(PARK7):​c.-23-4del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.061 in 115,136 control chromosomes in the GnomAD database, including 496 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.061 (496 hom., cov: 29)
  • Exomes 𝑓: 0.29 (19 hom.)
  • Failed GnomAD Quality Control
• Consequence: PARK7 NM_007262.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.11

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-7962740-CT-C is Benign according to our data. Variant chr1-7962740-CT-C is described in ClinVar as [Benign]. Clinvar id is 1234017.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.182 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARK7	NM_007262.5	c.-23-4del		intron_variant		ENST00000338639.10
PARK7	NM_001123377.2	c.-23-4del		intron_variant
PARK7	XM_005263424.4	c.-23-4del		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARK7	ENST00000338639.10	c.-23-4del		intron_variant		1	NM_007262.5	P1

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 7016 AN: 115148 Hom.: 496 Cov.: 29

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.00145

Gnomad AMR AF: 0.0312

Gnomad ASJ AF: 0.00400

Gnomad EAS AF: 0.00157

Gnomad SAS AF: 0.0188

Gnomad FIN AF: 0.0179

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.00651

Gnomad OTH AF: 0.0532

GnomAD3 exomes AF: 0.360 AC: 32426 AN: 89970 Hom.: 1 AF XY: 0.363 AC XY: 17941 AN XY: 49406

Gnomad AFR exome AF: 0.353

Gnomad AMR exome AF: 0.349

Gnomad ASJ exome AF: 0.391

Gnomad EAS exome AF: 0.345

Gnomad SAS exome AF: 0.386

Gnomad FIN exome AF: 0.345

Gnomad NFE exome AF: 0.359

Gnomad OTH exome AF: 0.350

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.288 AC: 288040 AN: 999166 Hom.: 19 Cov.: 0 AF XY: 0.291 AC XY: 146686 AN XY: 503940

Gnomad4 AFR exome AF: 0.328

Gnomad4 AMR exome AF: 0.282

Gnomad4 ASJ exome AF: 0.316

Gnomad4 EAS exome AF: 0.312

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.282

Gnomad4 NFE exome AF: 0.284

Gnomad4 OTH exome AF: 0.295

GnomAD4 genome AF: 0.0610 AC: 7024 AN: 115136 Hom.: 496 Cov.: 29 AF XY: 0.0618 AC XY: 3409 AN XY: 55122

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.0312

Gnomad4 ASJ AF: 0.00400

Gnomad4 EAS AF: 0.00157

Gnomad4 SAS AF: 0.0192

Gnomad4 FIN AF: 0.0179

Gnomad4 NFE AF: 0.00651

Gnomad4 OTH AF: 0.0531

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 22, 2020

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs370370394; hg19: chr1-8022800;