chr1-7962764-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_007262.5(PARK7):c.-22C>T variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00786 in 1,235,092 control chromosomes in the GnomAD database, including 546 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_007262.5 splice_region, 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PARK7 | NM_007262.5 | c.-22C>T | splice_region_variant, 5_prime_UTR_variant | 2/7 | ENST00000338639.10 | NP_009193.2 | ||
PARK7 | NM_001123377.2 | c.-22C>T | splice_region_variant, 5_prime_UTR_variant | 2/7 | NP_001116849.1 | |||
PARK7 | XM_005263424.4 | c.-22C>T | splice_region_variant, 5_prime_UTR_variant | 2/7 | XP_005263481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PARK7 | ENST00000338639.10 | c.-22C>T | splice_region_variant, 5_prime_UTR_variant | 2/7 | 1 | NM_007262.5 | ENSP00000340278 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0382 AC: 4959AN: 129676Hom.: 288 Cov.: 29
GnomAD3 exomes AF: 0.00965 AC: 2136AN: 221380Hom.: 107 AF XY: 0.00712 AC XY: 856AN XY: 120244
GnomAD4 exome AF: 0.00429 AC: 4737AN: 1105350Hom.: 257 Cov.: 20 AF XY: 0.00369 AC XY: 2070AN XY: 561640
GnomAD4 genome AF: 0.0383 AC: 4966AN: 129742Hom.: 289 Cov.: 29 AF XY: 0.0385 AC XY: 2374AN XY: 61644
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 17, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 30, 2020 | - - |
Autosomal recessive early-onset Parkinson disease 7 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at