rs1348969012
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001079537.2(TRAPPC6B):c.446-13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TRAPPC6B
NM_001079537.2 intron
NM_001079537.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.36
Publications
0 publications found
Genes affected
TRAPPC6B (HGNC:23066): (trafficking protein particle complex subunit 6B) TRAPPC6B is a component of TRAPP complexes, which are tethering complexes involved in vesicle transport (Kummel et al., 2005 [PubMed 16025134]).[supplied by OMIM, Mar 2008]
TRAPPC6B Gene-Disease associations (from GenCC):
- neurodevelopmental disorder with microcephaly, epilepsy, and brain atrophyInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Illumina, Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 14-39150394-A-G is Benign according to our data. Variant chr14-39150394-A-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3619156.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001079537.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TRAPPC6B | TSL:1 MANE Select | c.446-13T>C | intron | N/A | ENSP00000330289.5 | Q86SZ2-1 | |||
| TRAPPC6B | TSL:1 | c.362-13T>C | intron | N/A | ENSP00000335171.6 | Q86SZ2-2 | |||
| TRAPPC6B | TSL:1 | n.*326-13T>C | intron | N/A | ENSP00000452236.1 | G3V4C3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 207424 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
207424
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1364550Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 681078
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1364550
Hom.:
Cov.:
25
AF XY:
AC XY:
0
AN XY:
681078
African (AFR)
AF:
AC:
0
AN:
31348
American (AMR)
AF:
AC:
0
AN:
40036
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25034
East Asian (EAS)
AF:
AC:
0
AN:
39048
South Asian (SAS)
AF:
AC:
0
AN:
79182
European-Finnish (FIN)
AF:
AC:
0
AN:
40454
Middle Eastern (MID)
AF:
AC:
0
AN:
5588
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1046648
Other (OTH)
AF:
AC:
0
AN:
57212
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
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
Publications
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