15-23000076-C-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_052903.6(TUBGCP5):c.3029-210G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 151,736 control chromosomes in the GnomAD database, including 17,712 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.48 ( 17712 hom., cov: 32)
Consequence
TUBGCP5
NM_052903.6 intron
NM_052903.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0150
Genes affected
TUBGCP5 (HGNC:18600): (tubulin gamma complex component 5) Enables microtubule binding activity. Involved in microtubule nucleation. Located in centrosome and cytosol. Part of gamma-tubulin large complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BP6
Variant 15-23000076-C-A is Benign according to our data. Variant chr15-23000076-C-A is described in ClinVar as [Benign]. Clinvar id is 1288443.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBGCP5 | ENST00000615383.5 | c.3029-210G>T | intron_variant | Intron 22 of 22 | 1 | NM_052903.6 | ENSP00000480316.1 | |||
TUBGCP5 | ENST00000614508.4 | n.3028+493G>T | intron_variant | Intron 22 of 23 | 5 | ENSP00000484566.1 | ||||
TUBGCP5 | ENST00000620435.4 | c.*446G>T | downstream_gene_variant | 2 | ENSP00000481853.1 |
Frequencies
GnomAD3 genomes AF: 0.475 AC: 72002AN: 151618Hom.: 17679 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.475 AC: 72085AN: 151736Hom.: 17712 Cov.: 32 AF XY: 0.478 AC XY: 35449AN XY: 74108
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jun 19, 2021
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at