rs2833929
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_203446.3(SYNJ1):c.3518-7G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,613,026 control chromosomes in the GnomAD database, including 65,816 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_203446.3 splice_region, splice_polypyrimidine_tract, intron
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 | UniProt |
---|---|---|---|---|---|---|---|
SYNJ1 | NM_203446.3 | c.3518-7G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000674351.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNJ1 | ENST00000674351.1 | c.3518-7G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_203446.3 |
Frequencies
GnomAD3 genomes ? AF: 0.283 AC: 42907AN: 151788Hom.: 6106 Cov.: 31
GnomAD3 exomes AF: 0.289 AC: 72536AN: 250784Hom.: 10847 AF XY: 0.294 AC XY: 39844AN XY: 135608
GnomAD4 exome AF: 0.284 AC: 414806AN: 1461118Hom.: 59703 Cov.: 35 AF XY: 0.286 AC XY: 207711AN XY: 726904
GnomAD4 genome ? AF: 0.283 AC: 42932AN: 151908Hom.: 6113 Cov.: 31 AF XY: 0.283 AC XY: 20980AN XY: 74242
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 05, 2018 | - - |
Early-onset Parkinson disease 20;C4479313:Developmental and epileptic encephalopathy, 53 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Developmental and epileptic encephalopathy, 53 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Early-onset Parkinson disease 20 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at