1-7961850-GGTGCTGGACGGTGTCCCT-G

Position:

• chr1-7961850-GGTGCTGGACGGTGTCCCT-G

Variant summary

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

The NM_007262.5(PARK7):​c.-24+75_-24+92del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,158 control chromosomes in the GnomAD database, including 1,911 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1911 hom., cov: 30)
  • Exomes 𝑓: 0.026 (0 hom.)
• Consequence: PARK7 NM_007262.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.721

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 1-7961850-GGTGCTGGACGGTGTCCCT-G is Benign according to our data. Variant chr1-7961850-GGTGCTGGACGGTGTCCCT-G is described in ClinVar as [Benign]. Clinvar id is 1246972.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARK7	NM_007262.5	c.-24+75_-24+92del		intron_variant		ENST00000338639.10	NP_009193.2
PARK7	XM_005263424.4	c.-237_-220del		5_prime_UTR_variant	1/7		XP_005263481.1
PARK7	NM_001123377.2	c.-24+133_-24+150del		intron_variant			NP_001116849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10	c.-24+75_-24+92del		intron_variant		1	NM_007262.5	ENSP00000340278	P1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21183 AN: 151770 Hom.: 1909 Cov.: 30

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.129

GnomAD4 exome AF: 0.0257 AC: 7 AN: 272 Hom.: 0 AF XY: 0.0275 AC XY: 5 AN XY: 182

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0330

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.139 AC: 21179 AN: 151886 Hom.: 1911 Cov.: 30 AF XY: 0.142 AC XY: 10547 AN XY: 74220

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0742 Hom.: 105

Bravo AF: 0.123

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

Oct 04, 2019

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs200968609; hg19: chr1-8021910;