chr8-140458473-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The XM_011517326.3(TRAPPC9):c.92G>A(p.Arg31Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000563 in 1,420,050 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
XM_011517326.3 missense
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 |
---|---|---|---|---|---|---|---|
TRAPPC9 | XM_011517326.3 | c.92G>A | p.Arg31Gln | missense_variant | 1/22 | ||
TRAPPC9 | XM_011517328.3 | c.92G>A | p.Arg31Gln | missense_variant | 1/22 | ||
TRAPPC9 | XM_047422294.1 | c.92G>A | p.Arg31Gln | missense_variant | 1/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000648948.2 | c.-203G>A | 5_prime_UTR_variant | 1/23 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000572 AC: 1AN: 174764Hom.: 0 AF XY: 0.0000105 AC XY: 1AN XY: 94806
GnomAD4 exome AF: 0.00000563 AC: 8AN: 1420050Hom.: 0 Cov.: 34 AF XY: 0.00000427 AC XY: 3AN XY: 702774
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at