chr15-23005480-C-T

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_052903.6(TUBGCP5):​c.2664G>A​(p.Val888Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000731 in 1,614,192 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0040 ( 6 hom., cov: 32)
Exomes 𝑓: 0.00039 ( 5 hom. )

Consequence

TUBGCP5
NM_052903.6 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.64
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 -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.36).
BP6
Variant 15-23005480-C-T is Benign according to our data. Variant chr15-23005480-C-T is described in ClinVar as [Benign]. Clinvar id is 710289.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=1.64 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TUBGCP5NM_052903.6 linkc.2664G>A p.Val888Val synonymous_variant Exon 19 of 23 ENST00000615383.5 NP_443135.3 Q96RT8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TUBGCP5ENST00000615383.5 linkc.2664G>A p.Val888Val synonymous_variant Exon 19 of 23 1 NM_052903.6 ENSP00000480316.1 Q96RT8-1
TUBGCP5ENST00000620435.4 linkc.2664G>A p.Val888Val synonymous_variant Exon 19 of 22 2 ENSP00000481853.1 Q96RT8-2
TUBGCP5ENST00000610294.1 linkc.627G>A p.Val209Val synonymous_variant Exon 5 of 5 5 ENSP00000483015.1 A0A087X006
TUBGCP5ENST00000614508.4 linkn.2664G>A non_coding_transcript_exon_variant Exon 19 of 24 5 ENSP00000484566.1 A0A087X1Z1

Frequencies

GnomAD3 genomes
AF:
0.00404
AC:
615
AN:
152184
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0144
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000785
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00144
GnomAD3 exomes
AF:
0.00107
AC:
270
AN:
251452
Hom.:
4
AF XY:
0.000795
AC XY:
108
AN XY:
135900
show subpopulations
Gnomad AFR exome
AF:
0.0153
Gnomad AMR exome
AF:
0.000491
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.000489
GnomAD4 exome
AF:
0.000386
AC:
564
AN:
1461890
Hom.:
5
Cov.:
31
AF XY:
0.000318
AC XY:
231
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.0143
Gnomad4 AMR exome
AF:
0.000581
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000809
Gnomad4 OTH exome
AF:
0.000745
GnomAD4 genome
AF:
0.00404
AC:
616
AN:
152302
Hom.:
6
Cov.:
32
AF XY:
0.00379
AC XY:
282
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.0144
Gnomad4 AMR
AF:
0.000784
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00239
Hom.:
2
Bravo
AF:
0.00457
Asia WGS
AF:
0.00115
AC:
5
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
May 16, 2018
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.36
CADD
Benign
9.8
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

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: rs61739977; hg19: chr15-22867588; API