rs376206541
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_203446.3(SYNJ1):c.2875-5G>A 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 0.0000576 in 1,597,598 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Likely benign (★).
Frequency
Consequence
NM_203446.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYNJ1 | NM_203446.3 | c.2875-5G>A | 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.2875-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | NM_203446.3 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 151976Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000901 AC: 21AN: 233148Hom.: 0 AF XY: 0.0000872 AC XY: 11AN XY: 126154
GnomAD4 exome AF: 0.0000429 AC: 62AN: 1445504Hom.: 0 Cov.: 30 AF XY: 0.0000501 AC XY: 36AN XY: 718504
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152094Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74358
ClinVar
Submissions by phenotype
Early-onset Parkinson disease 20;C4479313:Developmental and epileptic encephalopathy, 53 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at