chr4-183679344-A-G
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 splice polypyrimidine tract, 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 splice_polypyrimidine_tract, intron
NM_021942.6 splice_polypyrimidine_tract, 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]
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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 GnomAd at 24 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAPPC11 | NM_021942.6 | c.832-9A>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000334690.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAPPC11 | ENST00000334690.11 | c.832-9A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_021942.6 | P1 | |||
TRAPPC11 | ENST00000357207.8 | c.832-9A>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
TRAPPC11 | ENST00000505676.5 | c.163-864A>G | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00889 AC: 1351AN: 152012Hom.: 24 Cov.: 33
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GnomAD3 exomes AF: 0.00243 AC: 518AN: 213072Hom.: 8 AF XY: 0.00189 AC XY: 219AN XY: 116062
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GnomAD4 exome AF: 0.000884 AC: 1243AN: 1406232Hom.: 21 Cov.: 30 AF XY: 0.000771 AC XY: 537AN XY: 696396
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GnomAD4 genome ? AF: 0.00893 AC: 1359AN: 152130Hom.: 24 Cov.: 33 AF XY: 0.00862 AC XY: 641AN XY: 74344
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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 | Invitae | 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