chr8-139732122-G-A

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6

The NM_001160372.4(TRAPPC9):​c.3136C>T​(p.Arg1046Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,605,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1046Q) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

TRAPPC9
NM_001160372.4 missense

Scores

6
13

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:4B:2

Conservation

PhyloP100: 1.60
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.048404127).
BP6
Variant 8-139732122-G-A is Benign according to our data. Variant chr8-139732122-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 362065.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=4}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TRAPPC9NM_001160372.4 linkuse as main transcriptc.3136C>T p.Arg1046Trp missense_variant 22/23 ENST00000438773.4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TRAPPC9ENST00000438773.4 linkuse as main transcriptc.3136C>T p.Arg1046Trp missense_variant 22/231 NM_001160372.4 P1Q96Q05-1

Frequencies

GnomAD3 genomes
AF:
0.000145
AC:
22
AN:
152192
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00403
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000279
AC:
65
AN:
232652
Hom.:
0
AF XY:
0.000277
AC XY:
35
AN XY:
126514
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000570
Gnomad ASJ exome
AF:
0.00332
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000105
Gnomad OTH exome
AF:
0.000525
GnomAD4 exome
AF:
0.000115
AC:
167
AN:
1453576
Hom.:
0
Cov.:
32
AF XY:
0.000127
AC XY:
92
AN XY:
722390
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.000545
Gnomad4 ASJ exome
AF:
0.00362
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000117
Gnomad4 OTH exome
AF:
0.000584
GnomAD4 genome
AF:
0.000145
AC:
22
AN:
152192
Hom.:
0
Cov.:
34
AF XY:
0.0000942
AC XY:
7
AN XY:
74344
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00403
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.000956
Alfa
AF:
0.000364
Hom.:
0
Bravo
AF:
0.000208
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000157
AC:
19

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:4Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 25, 2023- -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxDec 07, 2021In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoMay 03, 2016- -
Intellectual disability, autosomal recessive 13 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingBaylor GeneticsSep 28, 2018This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Intellectual Disability, Recessive Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJun 14, 2016- -
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsDec 15, 2021This 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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.098
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.21
CADD
Pathogenic
28
DANN
Uncertain
1.0
DEOGEN2
Benign
0.076
T;T;.;T
Eigen
Benign
0.18
Eigen_PC
Benign
0.16
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Uncertain
0.95
.;.;D;D
M_CAP
Benign
0.033
D
MetaRNN
Benign
0.048
T;T;T;T
MetaSVM
Benign
-0.72
T
MutationAssessor
Benign
0.34
N;N;.;N
MutationTaster
Benign
0.53
N;N;N
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-0.92
.;N;N;.
REVEL
Benign
0.23
Sift
Uncertain
0.022
.;D;T;.
Sift4G
Uncertain
0.029
.;D;D;.
Polyphen
1.0
D;D;D;D
Vest4
0.63, 0.66
MVP
0.44
MPC
0.42
ClinPred
0.095
T
GERP RS
2.4
Varity_R
0.12
gMVP
0.81

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.090
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs376617920; hg19: chr8-140744365; API