1-7961913-G-T

Variant names:

• chr1-7961913-G-T
• rs35675666
• NM_007262.5:c.-24+120G>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_007262.5(PARK7):​c.-24+120G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 152,330 control chromosomes in the GnomAD database, including 2,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.18 (2900 hom., cov: 33)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: PARK7 NM_007262.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.226
• Publications: 62 publications found

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 Gene-Disease associations (from GenCC):

• Parkinson disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive early-onset Parkinson disease 7

  Inheritance: AR Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• young-onset Parkinson disease

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 1-7961913-G-T is Benign according to our data. Variant chr1-7961913-G-T is described in ClinVar as Benign. ClinVar VariationId is 1243450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARK7	NM_007262.5	c.-24+120G>T		intron_variant	Intron 1 of 6	ENST00000338639.10	NP_009193.2
PARK7	XM_005263424.4	c.-192G>T		5_prime_UTR_variant	Exon 1 of 7		XP_005263481.1
PARK7	NM_001123377.2	c.-24+178G>T		intron_variant	Intron 1 of 6		NP_001116849.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARK7	ENST00000338639.10	c.-24+120G>T		intron_variant	Intron 1 of 6	1	NM_007262.5	ENSP00000340278.5

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28030 AN: 152054 Hom.: 2892 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.131 AC: 21 AN: 160 Hom.: 1 Cov.: 0 AF XY: 0.136 AC XY: 15 AN XY: 110

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 10

South Asian (SAS) AF: 0.125 AC: 1 AN: 8

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.137 AC: 17 AN: 124

Other (OTH) AF: 0.100 AC: 1 AN: 10

GnomAD4 genome AF: 0.184 AC: 28061 AN: 152170 Hom.: 2900 Cov.: 33 AF XY: 0.184 AC XY: 13728 AN XY: 74412

African (AFR) AF: 0.250 AC: 10393 AN: 41524

American (AMR) AF: 0.118 AC: 1805 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.0628 AC: 325 AN: 5178

South Asian (SAS) AF: 0.0957 AC: 462 AN: 4826

European-Finnish (FIN) AF: 0.287 AC: 3032 AN: 10578

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11270 AN: 67986

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.158 Hom.: 4472

Bravo AF: 0.178

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Aug 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.3
DANN	Benign	0.84
PhyloP100		0.23
PromoterAI		0.011	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=300/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs35675666; hg19: chr1-8021973;