Variant chr10-5393778-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The ENST00000380419.8(TUBAL3):c.1080G>A(p.Val360Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00184 in 1,614,216 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 11 hom. )

Consequence

TUBAL3
ENST00000380419.8 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0500

Variant links:

Genes affected

TUBAL3 (HGNC:23534): (tubulin alpha like 3) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Predicted to be active in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TUBAL3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP6

Variant 10-5393778-C-T is Benign according to our data. Variant chr10-5393778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640286.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.05 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBAL3	NM_024803.3 linkuse as main transcript	c.1080G>A	p.Val360Val	synonymous_variant	4/4	ENST00000380419.8	NP_079079.1	A6NHL2-1
TUBAL3	NM_001171864.2 linkuse as main transcript	c.960G>A	p.Val320Val	synonymous_variant	4/4		NP_001165335.1	A6NHL2-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBAL3	ENST00000380419.8 linkuse as main transcript	c.1080G>A	p.Val360Val	synonymous_variant	4/4	1	NM_024803.3	ENSP00000369784.3		A6NHL2-1
TUBAL3	ENST00000479328.1 linkuse as main transcript	c.960G>A	p.Val320Val	synonymous_variant	4/4	1		ENSP00000418799.1		A6NHL2-2

Frequencies

GnomAD3 genomes

AF:

0.00185

AC:

281

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000265

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000196

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00578

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.0131

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00128

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00254

AC:

639

AN:

251402

Hom.:

AF XY:

0.00272

AC XY:

370

AN XY:

135872

show subpopulations

Gnomad AFR exome

AF:

0.000185

Gnomad AMR exome

AF:

0.000347

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.00277

Gnomad SAS exome

AF:

0.00160

Gnomad FIN exome

AF:

0.0149

Gnomad NFE exome

AF:

0.00159

Gnomad OTH exome

AF:

0.00326

GnomAD4 exome

AF:

0.00183

AC:

2682

AN:

1461890

Hom.:

Cov.:

AF XY:

0.00189

AC XY:

1377

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.000269

Gnomad4 AMR exome

AF:

0.000291

Gnomad4 ASJ exome

AF:

0.000306

Gnomad4 EAS exome

AF:

0.0111

Gnomad4 SAS exome

AF:

0.00166

Gnomad4 FIN exome

AF:

0.0144

Gnomad4 NFE exome

AF:

0.00103

Gnomad4 OTH exome

AF:

0.00184

GnomAD4 genome

AF:

0.00184

AC:

281

AN:

152326

Hom.:

Cov.:

AF XY:

0.00232

AC XY:

173

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.000265

Gnomad4 AMR

AF:

0.000196

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00579

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0131

Gnomad4 NFE

AF:

0.00128

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00150

Hom.:

Bravo

AF:

0.000752

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.00104

EpiControl

AF:

0.00119

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

TUBAL3: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

6.7

DANN

Benign

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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