rs11781386
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_001160372.4(TRAPPC9):c.888T>A(p.Gly296=) variant causes a splice region, 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. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001160372.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC9 | NM_001160372.4 | c.888T>A | p.Gly296= | splice_region_variant, synonymous_variant | 6/23 | ENST00000438773.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000438773.4 | c.888T>A | p.Gly296= | splice_region_variant, synonymous_variant | 6/23 | 1 | NM_001160372.4 | P1 | |
TRAPPC9 | ENST00000520857.5 | c.420T>A | p.Gly140= | splice_region_variant, synonymous_variant | 4/21 | 1 | |||
TRAPPC9 | ENST00000648948.2 | c.888T>A | p.Gly296= | splice_region_variant, synonymous_variant | 6/23 | P1 | |||
TRAPPC9 | ENST00000521944.1 | n.88T>A | splice_region_variant, non_coding_transcript_exon_variant | 2/2 | 3 |
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