rs1057519269
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_001278512.2(AP3B2):c.1182G>A(p.Lys394=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.00000205 in 1,461,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars).
Frequency
Consequence
NM_001278512.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP3B2 | NM_001278512.2 | c.1182G>A | p.Lys394= | splice_region_variant, synonymous_variant | 10/27 | ENST00000535359.6 | |
CPEB1-AS1 | NR_046096.1 | n.1329-12282C>T | intron_variant, non_coding_transcript_variant | ||||
AP3B2 | NM_004644.5 | c.1182G>A | p.Lys394= | splice_region_variant, synonymous_variant | 10/26 | ||
AP3B2 | NM_001278511.2 | c.1086G>A | p.Lys362= | splice_region_variant, synonymous_variant | 9/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B2 | ENST00000535359.6 | c.1182G>A | p.Lys394= | splice_region_variant, synonymous_variant | 10/27 | 1 | NM_001278512.2 | ||
CPEB1-AS1 | ENST00000560650.1 | n.1329-12282C>T | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461272Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726952
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Epileptic encephalopathy Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | - | - - |
Developmental and epileptic encephalopathy, 48 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 19, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at