Variant chr6-30722488-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_178014.4(TUBB):c.58-49A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,253,436 control chromosomes in the GnomAD database, including 2,284 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.074 ( 670 hom., cov: 32)

Exomes 𝑓: 0.042 ( 1614 hom. )

Consequence

TUBB
NM_178014.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.169

Variant links:

Genes affected

TUBB (HGNC:20778): (tubulin beta class I) This gene encodes a beta tubulin protein. This protein forms a dimer with alpha tubulin and acts as a structural component of microtubules. Mutations in this gene cause cortical dysplasia, complex, with other brain malformations 6. Alternative splicing results in multiple splice variants. There are multiple pseudogenes for this gene on chromosomes 1, 6, 7, 8, 9, and 13. [provided by RefSeq, Jun 2014]

TUBB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

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

BP6

Variant 6-30722488-A-T is Benign according to our data. Variant chr6-30722488-A-T is described in ClinVar as [Benign]. Clinvar id is 1295941.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBB	NM_178014.4 linkuse as main transcript	c.58-49A>T		intron_variant		ENST00000327892.13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB	ENST00000327892.13 linkuse as main transcript	c.58-49A>T		intron_variant		1	NM_178014.4	P1

Frequencies

GnomAD3 genomes

AF:

0.0736

AC:

11198

AN:

152150

Hom.:

668

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0538

Gnomad ASJ

AF:

0.0516

Gnomad EAS

AF:

0.0805

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.130

Gnomad NFE

AF:

0.0353

Gnomad OTH

AF:

0.0731

GnomAD3 exomes

AF:

0.0558

AC:

12691

AN:

227276

Hom.:

571

AF XY:

0.0570

AC XY:

7052

AN XY:

123804

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.0327

Gnomad ASJ exome

AF:

0.0526

Gnomad EAS exome

AF:

0.108

Gnomad SAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.0108

Gnomad NFE exome

AF:

0.0358

Gnomad OTH exome

AF:

0.0593

GnomAD4 exome

AF:

0.0418

AC:

46060

AN:

1101168

Hom.:

1614

Cov.:

AF XY:

0.0436

AC XY:

24462

AN XY:

561068

show subpopulations

Gnomad4 AFR exome

AF:

0.156

Gnomad4 AMR exome

AF:

0.0368

Gnomad4 ASJ exome

AF:

0.0528

Gnomad4 EAS exome

AF:

0.0495

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.0125

Gnomad4 NFE exome

AF:

0.0327

Gnomad4 OTH exome

AF:

0.0526

GnomAD4 genome

AF:

0.0736

AC:

11206

AN:

152268

Hom.:

670

Cov.:

AF XY:

0.0731

AC XY:

5445

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.157

Gnomad4 AMR

AF:

0.0536

Gnomad4 ASJ

AF:

0.0516

Gnomad4 EAS

AF:

0.0803

Gnomad4 SAS

AF:

0.117

Gnomad4 FIN

AF:

0.0111

Gnomad4 NFE

AF:

0.0353

Gnomad4 OTH

AF:

0.0723

Alfa

AF:

0.0511

Hom.:

Bravo

AF:

0.0803

Asia WGS

AF:

0.120

AC:

415

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.0

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.3

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