chr5-78128123-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003664.5(AP3B1):c.1875T>C(p.Thr625=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T625T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003664.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AP3B1 | NM_003664.5 | c.1875T>C | p.Thr625= | synonymous_variant | 17/27 | ENST00000255194.11 | |
AP3B1 | NM_001271769.2 | c.1728T>C | p.Thr576= | synonymous_variant | 17/27 | ||
AP3B1 | NM_001410752.1 | c.1875T>C | p.Thr625= | synonymous_variant | 17/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AP3B1 | ENST00000255194.11 | c.1875T>C | p.Thr625= | synonymous_variant | 17/27 | 1 | NM_003664.5 | P2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at