Genetic Variant TUBGCP5:c.3028+299T>C (chr15-23000270-A-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_052903.6(TUBGCP5):c.3028+299T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 1,248,342 control chromosomes in the GnomAD database, including 9,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.089 ( 1074 hom., cov: 33)

Exomes 𝑓: 0.11 ( 8364 hom. )

Consequence

TUBGCP5
NM_052903.6 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.856

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]

TUBGCP5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.74).

BP6

Variant 15-23000270-A-G is Benign according to our data. Variant chr15-23000270-A-G is described in ClinVar as [Benign]. Clinvar id is 1282490.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBGCP5	NM_052903.6 link	c.3028+299T>C		intron_variant	Intron 22 of 22	ENST00000615383.5	NP_443135.3	Q96RT8-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TUBGCP5	ENST00000615383.5 link	c.3028+299T>C	intron_variant	Intron 22 of 22	1	NM_052903.6	ENSP00000480316.1	Q96RT8-1
TUBGCP5	ENST00000614508.4 link	n.3028+299T>C	intron_variant	Intron 22 of 23	5		ENSP00000484566.1	A0A087X1Z1
TUBGCP5	ENST00000620435.4 link	c.*252T>C	downstream_gene_variant		2		ENSP00000481853.1	Q96RT8-2

Frequencies

GnomAD3 genomes

AF:

0.0889

AC:

13524

AN:

152162

Hom.:

1074

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0421

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.0548

Gnomad ASJ

AF:

0.112

Gnomad EAS

AF:

0.457

Gnomad SAS

AF:

0.0832

Gnomad FIN

AF:

0.0924

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0958

Gnomad OTH

AF:

0.0756

GnomAD4 exome

AF:

0.107

AC:

117010

AN:

1096062

Hom.:

8364

Cov.:

AF XY:

0.106

AC XY:

55284

AN XY:

519106

show subpopulations

Gnomad4 AFR exome

AF:

0.0356

Gnomad4 AMR exome

AF:

0.0448

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.460

Gnomad4 SAS exome

AF:

0.0860

Gnomad4 FIN exome

AF:

0.0878

Gnomad4 NFE exome

AF:

0.100

Gnomad4 OTH exome

AF:

0.110

GnomAD4 genome

AF:

0.0888

AC:

13528

AN:

152280

Hom.:

1074

Cov.:

AF XY:

0.0903

AC XY:

6726

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0421

Gnomad4 AMR

AF:

0.0547

Gnomad4 ASJ

AF:

0.112

Gnomad4 EAS

AF:

0.458

Gnomad4 SAS

AF:

0.0835

Gnomad4 FIN

AF:

0.0924

Gnomad4 NFE

AF:

0.0958

Gnomad4 OTH

AF:

0.0767

Alfa

AF:

0.0914

Hom.:

312

Bravo

AF:

0.0857

Asia WGS

AF:

0.222

AC:

771

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

9.8

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over