rs79804817
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The ENST00000334690.11(TRAPPC11):c.3019G>A(p.Val1007Met) variant causes a missense change. The variant allele was found at a frequency of 0.00168 in 1,598,108 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0021 ( 6 hom., cov: 32)
Exomes 𝑓: 0.0016 ( 51 hom. )
Consequence
TRAPPC11
ENST00000334690.11 missense
ENST00000334690.11 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 6.22
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 (MetaRNN=0.0064311624).
BP6
Variant 4-183705034-G-A is Benign according to our data. Variant chr4-183705034-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 261453.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr4-183705034-G-A is described in Lovd as [Benign]. Variant chr4-183705034-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0021 (320/152236) while in subpopulation EAS AF= 0.0424 (219/5168). AF 95% confidence interval is 0.0378. There are 6 homozygotes in gnomad4. There are 180 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.3019G>A | p.Val1007Met | missense_variant | 27/30 | ENST00000334690.11 | NP_068761.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.3019G>A | p.Val1007Met | missense_variant | 27/30 | 1 | NM_021942.6 | ENSP00000335371 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00211 AC: 321AN: 152118Hom.: 6 Cov.: 32
GnomAD3 genomes
AF:
AC:
321
AN:
152118
Hom.:
Cov.:
32
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: 0.00427 AC: 1073AN: 251382Hom.: 27 AF XY: 0.00378 AC XY: 513AN XY: 135846
GnomAD3 exomes
AF:
AC:
1073
AN:
251382
Hom.:
AF XY:
AC XY:
513
AN XY:
135846
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: 0.00163 AC: 2361AN: 1445872Hom.: 51 Cov.: 29 AF XY: 0.00163 AC XY: 1174AN XY: 719436
GnomAD4 exome
AF:
AC:
2361
AN:
1445872
Hom.:
Cov.:
29
AF XY:
AC XY:
1174
AN XY:
719436
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: 0.00210 AC: 320AN: 152236Hom.: 6 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74436
GnomAD4 genome
AF:
AC:
320
AN:
152236
Hom.:
Cov.:
32
AF XY:
AC XY:
180
AN XY:
74436
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:
ESP6500AA
AF:
AC:
3
ESP6500EA
AF:
AC:
3
ExAC
AF:
AC:
470
Asia WGS
AF:
AC:
85
AN:
3478
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 | GeneDx | Feb 09, 2019 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
D;D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at