chr8-139731118-T-G
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001160372.4(TRAPPC9):āc.3390A>Cā(p.Pro1130=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000546 in 1,613,726 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Genomes: š 0.0030 ( 7 hom., cov: 33)
Exomes š: 0.00030 ( 4 hom. )
Consequence
TRAPPC9
NM_001160372.4 synonymous
NM_001160372.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.728
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 Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 8-139731118-T-G is Benign according to our data. Variant chr8-139731118-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 130618.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.728 with no splicing effect.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00295 (449/152146) while in subpopulation AFR AF= 0.0103 (429/41498). AF 95% confidence interval is 0.00953. There are 7 homozygotes in gnomad4. There are 203 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC9 | NM_001160372.4 | c.3390A>C | p.Pro1130= | synonymous_variant | 23/23 | ENST00000438773.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC9 | ENST00000438773.4 | c.3390A>C | p.Pro1130= | synonymous_variant | 23/23 | 1 | NM_001160372.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00295 AC: 448AN: 152028Hom.: 7 Cov.: 33
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GnomAD3 exomes AF: 0.000739 AC: 185AN: 250462Hom.: 0 AF XY: 0.000575 AC XY: 78AN XY: 135678
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GnomAD4 exome AF: 0.000296 AC: 432AN: 1461580Hom.: 4 Cov.: 31 AF XY: 0.000254 AC XY: 185AN XY: 727090
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GnomAD4 genome AF: 0.00295 AC: 449AN: 152146Hom.: 7 Cov.: 33 AF XY: 0.00273 AC XY: 203AN XY: 74388
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 24, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2023 | TRAPPC9: BP4, BP7, BS1, BS2 - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Nov 18, 2015 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
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