chr17-82929368-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005993.5(TBCD):c.2859T>C(p.Asp953=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 1,612,410 control chromosomes in the GnomAD database, including 50,838 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.25 ( 4698 hom., cov: 34)
Exomes 𝑓: 0.25 ( 46140 hom. )
Consequence
TBCD
NM_005993.5 synonymous
NM_005993.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.54
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BP6
?
Variant 17-82929368-T-C is Benign according to our data. Variant chr17-82929368-T-C is described in ClinVar as [Benign]. Clinvar id is 1167402.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-1.54 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TBCD | NM_005993.5 | c.2859T>C | p.Asp953= | synonymous_variant | 32/39 | ENST00000355528.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TBCD | ENST00000355528.9 | c.2859T>C | p.Asp953= | synonymous_variant | 32/39 | 1 | NM_005993.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.249 AC: 37819AN: 152070Hom.: 4693 Cov.: 34
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GnomAD3 exomes AF: 0.253 AC: 62652AN: 248076Hom.: 8040 AF XY: 0.252 AC XY: 33987AN XY: 134624
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GnomAD4 exome AF: 0.250 AC: 365007AN: 1460220Hom.: 46140 Cov.: 72 AF XY: 0.250 AC XY: 181425AN XY: 726268
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GnomAD4 genome ? AF: 0.249 AC: 37839AN: 152190Hom.: 4698 Cov.: 34 AF XY: 0.250 AC XY: 18578AN XY: 74388
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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 | GeneDx | May 05, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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