chr15-23000076-C-A

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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0150
Variant links:
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]

Genome browser will be placed here

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TUBGCP5NM_052903.6 linkc.3029-210G>T intron_variant Intron 22 of 22 ENST00000615383.5 NP_443135.3 Q96RT8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TUBGCP5ENST00000615383.5 linkc.3029-210G>T intron_variant Intron 22 of 22 1 NM_052903.6 ENSP00000480316.1 Q96RT8-1
TUBGCP5ENST00000614508.4 linkn.3028+493G>T intron_variant Intron 22 of 23 5 ENSP00000484566.1 A0A087X1Z1
TUBGCP5ENST00000620435.4 linkc.*446G>T downstream_gene_variant 2 ENSP00000481853.1 Q96RT8-2

Frequencies

GnomAD3 genomes
AF:
0.475
AC:
72002
AN:
151618
Hom.:
17679
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.573
Gnomad AMI
AF:
0.456
Gnomad AMR
AF:
0.347
Gnomad ASJ
AF:
0.478
Gnomad EAS
AF:
0.594
Gnomad SAS
AF:
0.499
Gnomad FIN
AF:
0.523
Gnomad MID
AF:
0.299
Gnomad NFE
AF:
0.427
Gnomad OTH
AF:
0.448
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.475
AC:
72085
AN:
151736
Hom.:
17712
Cov.:
32
AF XY:
0.478
AC XY:
35449
AN XY:
74108
show subpopulations
Gnomad4 AFR
AF:
0.574
Gnomad4 AMR
AF:
0.346
Gnomad4 ASJ
AF:
0.478
Gnomad4 EAS
AF:
0.594
Gnomad4 SAS
AF:
0.499
Gnomad4 FIN
AF:
0.523
Gnomad4 NFE
AF:
0.427
Gnomad4 OTH
AF:
0.448
Alfa
AF:
0.452
Hom.:
1961
Bravo
AF:
0.466
Asia WGS
AF:
0.547
AC:
1902
AN:
3478

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

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
1.0
DANN
Benign
0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11631470; hg19: chr15-22872992; API