Variant chr2-131479390-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.309C>T(p.Tyr103=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00235 in 149,196 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 0 hom., cov: 33)

Exomes 𝑓: 0.019 ( 3 hom. )

Failed GnomAD Quality Control

Consequence

TUBA3D
NM_080386.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.27

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=-0.71).

BP6

Variant 2-131479390-C-T is Benign according to our data. Variant chr2-131479390-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 791869.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.28 with no splicing effect.

BS2

High AC in GnomAd4 at 350 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TUBA3D	NM_080386.4 linkuse as main transcript	c.309C>T	p.Tyr103=	synonymous_variant	3/5	ENST00000321253.7
MZT2A	XM_005263742.4 linkuse as main transcript	c.320-7208G>A		intron_variant
MZT2A	XM_047445568.1 linkuse as main transcript	c.623-7208G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
TUBA3D	ENST00000321253.7 linkuse as main transcript	c.309C>T	p.Tyr103=	synonymous_variant	3/5	1	NM_080386.4	P1
TUBA3D	ENST00000409047.2 linkuse as main transcript	n.135C>T		non_coding_transcript_exon_variant	2/3	2
MZT2A	ENST00000427024.5 linkuse as main transcript	c.279-7208G>A		intron_variant, NMD_transcript_variant		3
MZT2A	ENST00000445782.2 linkuse as main transcript	n.331-7208G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.00232

AC:

346

AN:

149108

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00592

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00113

Gnomad ASJ

AF:

0.00231

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.0000944

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00123

Gnomad OTH

AF:

0.00243

GnomAD3 exomes

AF:

0.0957

AC:

16732

AN:

174766

Hom.:

AF XY:

0.0972

AC XY:

9080

AN XY:

93418

show subpopulations

Gnomad AFR exome

AF:

0.112

Gnomad AMR exome

AF:

0.0896

Gnomad ASJ exome

AF:

0.0743

Gnomad EAS exome

AF:

0.0805

Gnomad SAS exome

AF:

0.0959

Gnomad FIN exome

AF:

0.0818

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.0847

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0193

AC:

22833

AN:

1183232

Hom.:

Cov.:

AF XY:

0.0191

AC XY:

11319

AN XY:

592762

show subpopulations

Gnomad4 AFR exome

AF:

0.0461

Gnomad4 AMR exome

AF:

0.0207

Gnomad4 ASJ exome

AF:

0.0149

Gnomad4 EAS exome

AF:

0.00427

Gnomad4 SAS exome

AF:

0.0158

Gnomad4 FIN exome

AF:

0.00650

Gnomad4 NFE exome

AF:

0.0201

Gnomad4 OTH exome

AF:

0.0186

GnomAD4 genome

AF:

0.00235

AC:

350

AN:

149196

Hom.:

Cov.:

AF XY:

0.00258

AC XY:

188

AN XY:

72940

show subpopulations

Gnomad4 AFR

AF:

0.00601

Gnomad4 AMR

AF:

0.00113

Gnomad4 ASJ

AF:

0.00231

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.0000944

Gnomad4 NFE

AF:

0.00123

Gnomad4 OTH

AF:

0.00241

Alfa

AF:

0.0610

Hom.:

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

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

4.7

DANN

Benign

0.72

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