1-7962712-CAG-C

Position:

• chr1-7962712-CAG-C

Variant summary

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

The NM_007262.5(PARK7):​c.-23-50_-23-49del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,246,870 control chromosomes in the GnomAD database, including 17,833 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.19 (2895 hom., cov: 25)
  • Exomes 𝑓: 0.15 (14938 hom.)
• Consequence: PARK7 NM_007262.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.419

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 1-7962712-CAG-C is Benign according to our data. Variant chr1-7962712-CAG-C is described in ClinVar as [Benign]. Clinvar id is 1289619.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARK7	NM_007262.5	c.-23-50_-23-49del		intron_variant		ENST00000338639.10	NP_009193.2
PARK7	NM_001123377.2	c.-23-50_-23-49del		intron_variant			NP_001116849.1
PARK7	XM_005263424.4	c.-23-50_-23-49del		intron_variant			XP_005263481.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10	c.-23-50_-23-49del		intron_variant		1	NM_007262.5	ENSP00000340278	P1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 27884 AN: 149360 Hom.: 2887 Cov.: 25

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.0410

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.0973

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.0942

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.153 AC: 168202 AN: 1097412 Hom.: 14938 AF XY: 0.150 AC XY: 83551 AN XY: 555436

Gnomad4 AFR exome AF: 0.244

Gnomad4 AMR exome AF: 0.0986

Gnomad4 ASJ exome AF: 0.0967

Gnomad4 EAS exome AF: 0.0602

Gnomad4 SAS exome AF: 0.0936

Gnomad4 FIN exome AF: 0.259

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.140

GnomAD4 genome AF: 0.187 AC: 27915 AN: 149458 Hom.: 2895 Cov.: 25 AF XY: 0.187 AC XY: 13600 AN XY: 72736

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.0644

Gnomad4 SAS AF: 0.0970

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.163

Alfa AF: 0.189 Hom.: 376

Bravo AF: 0.182

Asia WGS AF: 0.0860 AC: 299 AN: 3478

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 14, 2018

- -

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: rs144768319; hg19: chr1-8022772;