NM_005993.5:c.44_46delAGG
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_005993.5(TBCD):c.44_46delAGG(p.Glu15del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000655 in 1,526,148 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000058 ( 0 hom. )
Consequence
TBCD
NM_005993.5 disruptive_inframe_deletion
NM_005993.5 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.10
Publications
0 publications found
Genes affected
TBCD (HGNC:11581): (tubulin folding cofactor D) Cofactor D is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. [provided by RefSeq, Jul 2008]
TBCD Gene-Disease associations (from GenCC):
- early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, PanelApp Australia, Labcorp Genetics (formerly Invitae), G2P, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_005993.5. Strenght limited to Supporting due to length of the change: 1aa.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005993.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TBCD | NM_005993.5 | MANE Select | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 39 | NP_005984.3 | ||
| TBCD | NM_001411101.1 | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 38 | NP_001398030.1 | A0A804HLI2 | ||
| TBCD | NM_001411102.1 | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 38 | NP_001398031.1 | A0A804HJ32 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| TBCD | ENST00000355528.9 | TSL:1 MANE Select | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 39 | ENSP00000347719.4 | Q9BTW9-1 | |
| TBCD | ENST00000684760.1 | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 40 | ENSP00000507696.1 | A0A804HJY5 | ||
| TBCD | ENST00000684349.1 | c.44_46delAGG | p.Glu15del | disruptive_inframe_deletion | Exon 1 of 39 | ENSP00000508067.1 | A0A804HKT8 |
Frequencies
GnomAD3 genomes 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
2
AN:
152114
Hom.:
Cov.:
33
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:
GnomAD4 exome AF: 0.00000582 AC: 8AN: 1374034Hom.: 0 AF XY: 0.00000885 AC XY: 6AN XY: 678034 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
1374034
Hom.:
AF XY:
AC XY:
6
AN XY:
678034
show subpopulations
African (AFR)
AF:
AC:
0
AN:
28408
American (AMR)
AF:
AC:
0
AN:
34236
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
24442
East Asian (EAS)
AF:
AC:
0
AN:
32706
South Asian (SAS)
AF:
AC:
0
AN:
77714
European-Finnish (FIN)
AF:
AC:
0
AN:
43164
Middle Eastern (MID)
AF:
AC:
0
AN:
4376
European-Non Finnish (NFE)
AF:
AC:
8
AN:
1071972
Other (OTH)
AF:
AC:
0
AN:
57016
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.0000131 AC: 2AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74324 show subpopulations
GnomAD4 genome
AF:
AC:
2
AN:
152114
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
74324
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41442
American (AMR)
AF:
AC:
0
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4838
European-Finnish (FIN)
AF:
AC:
0
AN:
10596
Middle Eastern (MID)
AF:
AC:
0
AN:
314
European-Non Finnish (NFE)
AF:
AC:
1
AN:
67976
Other (OTH)
AF:
AC:
0
AN:
2094
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
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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