rs886041053
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP3PP5_Moderate
The NM_021942.6(TRAPPC11):c.1893+3A>G variant causes a splice region, intron change. The variant allele was found at a frequency of 0.00000616 in 1,461,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000062 ( 0 hom. )
Consequence
TRAPPC11
NM_021942.6 splice_region, intron
NM_021942.6 splice_region, intron
Scores
2
Splicing: ADA: 0.9974
2
Clinical Significance
Conservation
PhyloP100: 6.97
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 Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
PP5
Variant 4-183686751-A-G is Pathogenic according to our data. Variant chr4-183686751-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 268055.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr4-183686751-A-G is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| TRAPPC11 | ENST00000334690.11 | c.1893+3A>G | splice_region_variant, intron_variant | Intron 18 of 29 | 1 | NM_021942.6 | ENSP00000335371.6 | |||
| TRAPPC11 | ENST00000357207.8 | c.1893+3A>G | splice_region_variant, intron_variant | Intron 18 of 30 | 1 | ENSP00000349738.4 | ||||
| TRAPPC11 | ENST00000512476.1 | c.711+3A>G | splice_region_variant, intron_variant | Intron 7 of 18 | 1 | ENSP00000421004.1 | ||||
| TRAPPC11 | ENST00000505676.5 | n.*7+3A>G | splice_region_variant, intron_variant | Intron 6 of 18 | 1 | ENSP00000422915.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461534Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727096
GnomAD4 exome
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AC:
9
AN:
1461534
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Cov.:
31
AF XY:
AC XY:
7
AN XY:
727096
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type R18 Pathogenic:2
Mar 05, 2020
Revvity Omics, Revvity
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Sep 25, 2018
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DL_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at