1-7962740-CTTTTTTTT-CTT

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_007262.5(PARK7):​c.-23-9_-23-4delTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,153,652 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000087 ( 0 hom., cov: 29)
Exomes 𝑓: 0.0000087 ( 0 hom. )

Consequence

PARK7
NM_007262.5 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.11
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PARK7NM_007262.5 linkc.-23-9_-23-4delTTTTTT splice_region_variant, intron_variant Intron 1 of 6 ENST00000338639.10 NP_009193.2 Q99497V9HWC2
PARK7NM_001123377.2 linkc.-23-9_-23-4delTTTTTT splice_region_variant, intron_variant Intron 1 of 6 NP_001116849.1 Q99497V9HWC2
PARK7XM_005263424.4 linkc.-23-9_-23-4delTTTTTT splice_region_variant, intron_variant Intron 1 of 6 XP_005263481.1 Q99497V9HWC2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PARK7ENST00000338639.10 linkc.-23-22_-23-17delTTTTTT intron_variant Intron 1 of 6 1 NM_007262.5 ENSP00000340278.5 Q99497

Frequencies

GnomAD3 genomes
AF:
0.00000868
AC:
1
AN:
115208
Hom.:
0
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000262
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000867
AC:
9
AN:
1038444
Hom.:
0
AF XY:
0.00000951
AC XY:
5
AN XY:
525734
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000914
Gnomad4 SAS exome
AF:
0.0000151
Gnomad4 FIN exome
AF:
0.0000282
Gnomad4 NFE exome
AF:
0.00000510
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000868
AC:
1
AN:
115208
Hom.:
0
Cov.:
29
AF XY:
0.0000181
AC XY:
1
AN XY:
55140
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000262
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs370370394; hg19: chr1-8022800; API