2-44323413-TA-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001171613.2(PREPL):c.1480-3del 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 0.0000823 in 1,567,254 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001171613.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PREPL | NM_001171613.2 | c.1480-3del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000409411.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PREPL | ENST00000409411.6 | c.1480-3del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001171613.2 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000198 AC: 3AN: 151522Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000890 AC: 126AN: 1415732Hom.: 0 Cov.: 30 AF XY: 0.0000866 AC XY: 61AN XY: 704212
GnomAD4 genome AF: 0.0000198 AC: 3AN: 151522Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73974
ClinVar
Submissions by phenotype
Myasthenic syndrome, congenital, 22 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at