rs114748616
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021942.6(TRAPPC11):c.832-9A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00167 in 1,558,362 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0089 ( 24 hom., cov: 33)
Exomes 𝑓: 0.00088 ( 21 hom. )
Consequence
TRAPPC11
NM_021942.6 intron
NM_021942.6 intron
Scores
2
Splicing: ADA: 0.0001246
2
Clinical Significance
Conservation
PhyloP100: -0.401
Genes affected
TRAPPC11 (HGNC:25751): (trafficking protein particle complex subunit 11) The protein encoded by this gene is a subunit of the TRAPP (transport protein particle) tethering complex, which functions in intracellular vesicle trafficking. This subunit is involved in early stage endoplasmic reticulum-to-Golgi vesicle transport. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 4-183679344-A-G is Benign according to our data. Variant chr4-183679344-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 448701.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00893 (1359/152130) while in subpopulation AFR AF= 0.0311 (1292/41512). AF 95% confidence interval is 0.0297. There are 24 homozygotes in gnomad4. There are 641 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.832-9A>G | intron_variant | ENST00000334690.11 | NP_068761.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.832-9A>G | intron_variant | 1 | NM_021942.6 | ENSP00000335371.6 | ||||
TRAPPC11 | ENST00000357207.8 | c.832-9A>G | intron_variant | 1 | ENSP00000349738.4 | |||||
TRAPPC11 | ENST00000505676.5 | n.163-864A>G | intron_variant | 1 | ENSP00000422915.1 |
Frequencies
GnomAD3 genomes AF: 0.00889 AC: 1351AN: 152012Hom.: 24 Cov.: 33
GnomAD3 genomes
AF:
AC:
1351
AN:
152012
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00243 AC: 518AN: 213072Hom.: 8 AF XY: 0.00189 AC XY: 219AN XY: 116062
GnomAD3 exomes
AF:
AC:
518
AN:
213072
Hom.:
AF XY:
AC XY:
219
AN XY:
116062
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000884 AC: 1243AN: 1406232Hom.: 21 Cov.: 30 AF XY: 0.000771 AC XY: 537AN XY: 696396
GnomAD4 exome
AF:
AC:
1243
AN:
1406232
Hom.:
Cov.:
30
AF XY:
AC XY:
537
AN XY:
696396
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00893 AC: 1359AN: 152130Hom.: 24 Cov.: 33 AF XY: 0.00862 AC XY: 641AN XY: 74344
GnomAD4 genome
AF:
AC:
1359
AN:
152130
Hom.:
Cov.:
33
AF XY:
AC XY:
641
AN XY:
74344
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
10
AN:
3478
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Sep 15, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 03, 2020 | - - |
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 19, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at