Genetic Variant TUBA3E:p.Arg422Arg (chr2-130191918-G-A) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_207312.3(TUBA3E):c.1266C>T(p.Arg422Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 1,610,554 control chromosomes in the GnomAD database, including 127,171 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.39 ( 11808 hom., cov: 30)

Exomes 𝑓: 0.40 ( 115363 hom. )

Consequence

TUBA3E
NM_207312.3 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.08

Variant links:

Genes affected

TUBA3E (HGNC:20765): (tubulin alpha 3e) Microtubules of the eukaryotic cytoskeleton perform essential and diverse functions and are composed of a heterodimer of alpha and beta tubulin. The genes encoding these microtubule constituents are part of the tubulin superfamily, which is composed of six distinct families. Genes from the alpha, beta and gamma tubulin families are found in all eukaryotes. The alpha and beta tubulins represent the major components of microtubules, while gamma tubulin plays a critical role in the nucleation of microtubule assembly. This gene encodes an alpha tubulin that highly conserved among species. A missense mutation in this gene has been potentially linked to microlissencephaly and global developmental delay. [provided by RefSeq, Jul 2016]

TUBA3E links:

MZT2B (HGNC:25886): (mitotic spindle organizing protein 2B) Located in cytosol; microtubule cytoskeleton; and nucleoplasm. Part of gamma-tubulin large complex. [provided by Alliance of Genome Resources, Apr 2022]

MZT2B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 2-130191918-G-A is Benign according to our data. Variant chr2-130191918-G-A is described in ClinVar as [Benign]. Clinvar id is 767820.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.08 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBA3E	NM_207312.3 link	c.1266C>T	p.Arg422Arg	synonymous_variant	Exon 5 of 5	ENST00000312988.9	NP_997195.2	Q6PEY2
MZT2B	XM_047445914.1 link	c.319+9143G>A		intron_variant	Intron 2 of 3		XP_047301870.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBA3E	ENST00000312988.9 link	c.1266C>T	p.Arg422Arg	synonymous_variant	Exon 5 of 5	1	NM_207312.3	ENSP00000318197.7		Q6PEY2

Frequencies

GnomAD3 genomes

AF:

0.391

AC:

59194

AN:

151458

Hom.:

11805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.350

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.470

Gnomad ASJ

AF:

0.338

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.412

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.397

Gnomad OTH

AF:

0.379

GnomAD3 exomes

AF:

0.407

AC:

101925

AN:

250706

Hom.:

21089

AF XY:

0.406

AC XY:

54936

AN XY:

135458

show subpopulations

Gnomad AFR exome

AF:

0.341

Gnomad AMR exome

AF:

0.452

Gnomad ASJ exome

AF:

0.333

Gnomad EAS exome

AF:

0.464

Gnomad SAS exome

AF:

0.407

Gnomad FIN exome

AF:

0.396

Gnomad NFE exome

AF:

0.401

Gnomad OTH exome

AF:

0.416

GnomAD4 exome

AF:

0.396

AC:

578044

AN:

1458976

Hom.:

115363

Cov.:

AF XY:

0.395

AC XY:

286491

AN XY:

725246

show subpopulations

Gnomad4 AFR exome

AF:

0.341

Gnomad4 AMR exome

AF:

0.455

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.419

Gnomad4 SAS exome

AF:

0.405

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.396

Gnomad4 OTH exome

AF:

0.395

GnomAD4 genome

AF:

0.391

AC:

59225

AN:

151578

Hom.:

11808

Cov.:

AF XY:

0.393

AC XY:

29125

AN XY:

74022

show subpopulations

Gnomad4 AFR

AF:

0.350

Gnomad4 AMR

AF:

0.470

Gnomad4 ASJ

AF:

0.338

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.411

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.397

Gnomad4 OTH

AF:

0.380

Alfa

AF:

0.386

Hom.:

3630

Bravo

AF:

0.395

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

- -

Jan 12, 2018

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.82

CADD

Benign

2.4

DANN

Benign

0.86

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