Genetic Variant TUBGCP5:c.1487+148C>T (chr15-23019071-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_052903.6(TUBGCP5):c.1487+148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 524,640 control chromosomes in the GnomAD database, including 120,788 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.72 ( 40428 hom., cov: 34)

Exomes 𝑓: 0.65 ( 80360 hom. )

Consequence

TUBGCP5
NM_052903.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.108

Publications

7 publications found

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 was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 15-23019071-G-A is Benign according to our data. Variant chr15-23019071-G-A is described in ClinVar as Benign. ClinVar VariationId is 1245202.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052903.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TUBGCP5	NM_052903.6	MANE Select	c.1487+148C>T	intron	N/A	NP_443135.3
TUBGCP5	NM_001354372.2		c.1490+148C>T	intron	N/A	NP_001341301.1
TUBGCP5	NM_001354373.2		c.1487+148C>T	intron	N/A	NP_001341302.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
TUBGCP5	ENST00000615383.5	TSL:1 MANE Select	c.1487+148C>T	intron	N/A	ENSP00000480316.1
TUBGCP5	ENST00000620435.4	TSL:2	c.1487+148C>T	intron	N/A	ENSP00000481853.1
TUBGCP5	ENST00000614508.4	TSL:5	n.1487+148C>T	intron	N/A	ENSP00000484566.1

Frequencies

GnomAD3 genomes

AF:

0.716

AC:

108939

AN:

152054

Hom.:

40377

Cov.:

show subpopulations

Gnomad AFR

AF:

0.919

Gnomad AMI

AF:

0.671

Gnomad AMR

AF:

0.579

Gnomad ASJ

AF:

0.670

Gnomad EAS

AF:

0.758

Gnomad SAS

AF:

0.672

Gnomad FIN

AF:

0.642

Gnomad MID

AF:

0.564

Gnomad NFE

AF:

0.640

Gnomad OTH

AF:

0.682

GnomAD4 exome

AF:

0.652

AC:

242897

AN:

372468

Hom.:

80360

AF XY:

0.653

AC XY:

125233

AN XY:

191824

show subpopulations

African (AFR)

AF:

0.912

AC:

9586

AN:

10510

American (AMR)

AF:

0.518

AC:

6892

AN:

13308

Ashkenazi Jewish (ASJ)

AF:

0.662

AC:

7746

AN:

11698

East Asian (EAS)

AF:

0.753

AC:

20800

AN:

27610

South Asian (SAS)

AF:

0.660

AC:

14810

AN:

22428

European-Finnish (FIN)

AF:

0.625

AC:

18993

AN:

30386

Middle Eastern (MID)

AF:

0.627

AC:

1115

AN:

1778

European-Non Finnish (NFE)

AF:

0.638

AC:

148372

AN:

232560

Other (OTH)

AF:

0.657

AC:

14583

AN:

22190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4064

8128

12192

16256

20320

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1058

2116

3174

4232

5290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.717

AC:

109040

AN:

152172

Hom.:

40428

Cov.:

AF XY:

0.714

AC XY:

53109

AN XY:

74378

show subpopulations

African (AFR)

AF:

0.919

AC:

38194

AN:

41548

American (AMR)

AF:

0.578

AC:

8841

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.670

AC:

2325

AN:

3470

East Asian (EAS)

AF:

0.758

AC:

3921

AN:

5176

South Asian (SAS)

AF:

0.672

AC:

3245

AN:

4830

European-Finnish (FIN)

AF:

0.642

AC:

6784

AN:

10574

Middle Eastern (MID)

AF:

0.558

AC:

163

AN:

292

European-Non Finnish (NFE)

AF:

0.640

AC:

43526

AN:

67976

Other (OTH)

AF:

0.678

AC:

1434

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1471

2942

4412

5883

7354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

822

1644

2466

3288

4110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.660

Hom.:

62333

Bravo

AF:

0.715

Asia WGS

AF:

0.714

AC:

2484

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

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.1

(source)

DANN

Benign

0.77

PhyloP100

0.11

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over