rs78663235
Positions:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_021942.6(TRAPPC11):āc.3310A>Gā(p.Thr1104Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000787 in 1,614,100 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.0045 ( 6 hom., cov: 33)
Exomes š: 0.00040 ( 5 hom. )
Consequence
TRAPPC11
NM_021942.6 missense
NM_021942.6 missense
Scores
1
1
16
Clinical Significance
Conservation
PhyloP100: 3.85
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0055687726).
BP6
?
Variant 4-183708527-A-G is Benign according to our data. Variant chr4-183708527-A-G is described in ClinVar as [Benign]. Clinvar id is 474355.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
?
High Homozygotes in GnomAd4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.3310A>G | p.Thr1104Ala | missense_variant | 29/30 | ENST00000334690.11 | |
TRAPPC11 | XM_024454179.2 | c.3310A>G | p.Thr1104Ala | missense_variant | 29/30 | ||
TRAPPC11 | XM_024454180.2 | c.3310A>G | p.Thr1104Ala | missense_variant | 30/31 | ||
TRAPPC11 | NM_199053.3 | c.3200-9A>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.3310A>G | p.Thr1104Ala | missense_variant | 29/30 | 1 | NM_021942.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00442 AC: 673AN: 152176Hom.: 6 Cov.: 33
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GnomAD3 exomes AF: 0.00114 AC: 286AN: 251338Hom.: 4 AF XY: 0.000832 AC XY: 113AN XY: 135848
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GnomAD4 exome AF: 0.000405 AC: 592AN: 1461806Hom.: 5 Cov.: 31 AF XY: 0.000312 AC XY: 227AN XY: 727206
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GnomAD4 genome ? AF: 0.00446 AC: 679AN: 152294Hom.: 6 Cov.: 33 AF XY: 0.00432 AC XY: 322AN XY: 74466
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ExAC
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Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 30, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 30, 2018 | This variant is associated with the following publications: (PMID: 29855340, 27862579) - |
Autosomal recessive limb-girdle muscular dystrophy type R18 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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