rs587780484
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_001160372.4(TRAPPC9):c.1194C>T(p.Ile398=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000144 in 1,614,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
TRAPPC9
NM_001160372.4 synonymous
NM_001160372.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.459
Genes affected
TRAPPC9 (HGNC:30832): (trafficking protein particle complex subunit 9) This gene encodes a protein that likely plays a role in NF-kappa-B signaling. Mutations in this gene have been associated with autosomal-recessive cognitive disability. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
Variant 8-140371121-G-A is Benign according to our data. Variant chr8-140371121-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 130620.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=3, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=-0.459 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC9 | NM_001160372.4 | c.1194C>T | p.Ile398= | synonymous_variant | 8/23 | ENST00000438773.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000438773.4 | c.1194C>T | p.Ile398= | synonymous_variant | 8/23 | 1 | NM_001160372.4 | P1 | |
TRAPPC9 | ENST00000520857.5 | c.726C>T | p.Ile242= | synonymous_variant | 6/21 | 1 | |||
TRAPPC9 | ENST00000648948.2 | c.1194C>T | p.Ile398= | synonymous_variant | 8/23 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152282Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000140 AC: 35AN: 250398Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135432
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GnomAD4 exome AF: 0.000146 AC: 214AN: 1461748Hom.: 0 Cov.: 32 AF XY: 0.000158 AC XY: 115AN XY: 727186
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GnomAD4 genome AF: 0.000125 AC: 19AN: 152400Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74530
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:1Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | TRAPPC9: BP4, BP7 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 01, 2013 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 24, 2023 | - - |
TRAPPC9-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at