chr1-7962740-CTT-C

Position:

• chr1-7962740-CTT-C

Variant summary

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

The NM_007262.5(PARK7):​c.-23-5_-23-4del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0334 in 1,107,842 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00053 (0 hom., cov: 29)
  • Exomes 𝑓: 0.037 (0 hom.)
• 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-CTT-C is Benign according to our data. Variant chr1-7962740-CTT-C is described in ClinVar as [Benign]. Clinvar id is 1229912.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0629 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.000530 AC: 61 AN: 115110 Hom.: 0 Cov.: 29

Gnomad AFR AF: 0.000862

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000268

Gnomad ASJ AF: 0.000363

Gnomad EAS AF: 0.000262

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00225

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000227

Gnomad OTH AF: 0.00133

GnomAD3 exomes AF: 0.0481 AC: 4325 AN: 89970 Hom.: 0 AF XY: 0.0486 AC XY: 2400 AN XY: 49406

Gnomad AFR exome AF: 0.0790

Gnomad AMR exome AF: 0.0531

Gnomad ASJ exome AF: 0.0317

Gnomad EAS exome AF: 0.0488

Gnomad SAS exome AF: 0.0365

Gnomad FIN exome AF: 0.0521

Gnomad NFE exome AF: 0.0475

Gnomad OTH exome AF: 0.0474

GnomAD4 exome AF: 0.0372 AC: 36939 AN: 992744 Hom.: 0 AF XY: 0.0365 AC XY: 18333 AN XY: 502248

Gnomad4 AFR exome AF: 0.0657

Gnomad4 AMR exome AF: 0.0426

Gnomad4 ASJ exome AF: 0.0389

Gnomad4 EAS exome AF: 0.0416

Gnomad4 SAS exome AF: 0.0275

Gnomad4 FIN exome AF: 0.0417

Gnomad4 NFE exome AF: 0.0364

Gnomad4 OTH exome AF: 0.0407

GnomAD4 genome AF: 0.000530 AC: 61 AN: 115098 Hom.: 0 Cov.: 29 AF XY: 0.000526 AC XY: 29 AN XY: 55106

Gnomad4 AFR AF: 0.000861

Gnomad4 AMR AF: 0.000268

Gnomad4 ASJ AF: 0.000363

Gnomad4 EAS AF: 0.000263

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00225

Gnomad4 NFE AF: 0.000227

Gnomad4 OTH AF: 0.00133

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

May 23, 2021

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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;