Variant chr2-131480542-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_080386.4(TUBA3D):c.849C>T(p.His283=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00228 in 1,607,258 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0017 ( 5 hom., cov: 30)

Exomes 𝑓: 0.0023 ( 64 hom. )

Consequence

TUBA3D
NM_080386.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.791

Variant links:

Genes affected

TUBA3D (HGNC:24071): (tubulin alpha 3d) This gene encodes a member of the alpha tubulin family. Tubulin is a major component of microtubules, which are composed of alpha- and beta-tubulin heterodimers and microtubule-associated proteins in the cytoskeleton. Microtubules maintain cellular structure, function in intracellular transport, and play a role in spindle formation during mitosis. [provided by RefSeq, Oct 2011]

TUBA3D links:

MZT2A (HGNC:33187): (mitotic spindle organizing protein 2A) Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MZT2A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 2-131480542-C-T is Benign according to our data. Variant chr2-131480542-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3024874.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.791 with no splicing effect.

BS2

High AC in GnomAd4 at 249 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TUBA3D	NM_080386.4 linkuse as main transcript	c.849C>T	p.His283=	synonymous_variant	4/5	ENST00000321253.7
MZT2A	XM_005263742.4 linkuse as main transcript	c.320-8360G>A		intron_variant
MZT2A	XM_047445568.1 linkuse as main transcript	c.623-8360G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TUBA3D	ENST00000321253.7 linkuse as main transcript	c.849C>T	p.His283=	synonymous_variant	4/5	1	NM_080386.4	P1
MZT2A	ENST00000427024.5 linkuse as main transcript	c.279-8360G>A		intron_variant, NMD_transcript_variant		3
MZT2A	ENST00000445782.2 linkuse as main transcript	n.331-8360G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00169

AC:

249

AN:

147420

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000644

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00106

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00425

Gnomad SAS

AF:

0.00653

Gnomad FIN

AF:

0.00152

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.00189

Gnomad OTH

AF:

0.00442

GnomAD3 exomes

AF:

0.00259

AC:

649

AN:

250410

Hom.:

AF XY:

0.00294

AC XY:

398

AN XY:

135460

show subpopulations

Gnomad AFR exome

AF:

0.00108

Gnomad AMR exome

AF:

0.00208

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.00409

Gnomad SAS exome

AF:

0.00768

Gnomad FIN exome

AF:

0.00139

Gnomad NFE exome

AF:

0.00177

Gnomad OTH exome

AF:

0.00278

GnomAD4 exome

AF:

0.00234

AC:

3415

AN:

1459726

Hom.:

Cov.:

AF XY:

0.00251

AC XY:

1826

AN XY:

726156

show subpopulations

Gnomad4 AFR exome

AF:

0.00125

Gnomad4 AMR exome

AF:

0.00197

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.00370

Gnomad4 SAS exome

AF:

0.00683

Gnomad4 FIN exome

AF:

0.00101

Gnomad4 NFE exome

AF:

0.00211

Gnomad4 OTH exome

AF:

0.00194

GnomAD4 genome

AF:

0.00169

AC:

249

AN:

147532

Hom.:

Cov.:

AF XY:

0.00178

AC XY:

128

AN XY:

72052

show subpopulations

Gnomad4 AFR

AF:

0.000642

Gnomad4 AMR

AF:

0.00106

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00426

Gnomad4 SAS

AF:

0.00654

Gnomad4 FIN

AF:

0.00152

Gnomad4 NFE

AF:

0.00189

Gnomad4 OTH

AF:

0.00437

Alfa

AF:

0.00204

Hom.:

EpiCase

AF:

0.00180

EpiControl

AF:

0.00190

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

Jan 01, 2024

TUBA3D: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

8.7

DANN

Benign

0.75

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