Variant 6-30720650-G-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.57+87G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,155,722 control chromosomes in the GnomAD database, including 29,058 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 6353 hom., cov: 32)

Exomes 𝑓: 0.20 ( 22705 hom. )

Consequence

TUBB
NM_178014.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.782

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 6-30720650-G-T is Benign according to our data. Variant chr6-30720650-G-T is described in ClinVar as [Benign]. Clinvar id is 1240826.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
TUBB	NM_178014.4 linkuse as main transcript	c.57+87G>T	intron_variant	ENST00000327892.13
TUBB	NM_001293213.2 linkuse as main transcript	c.57+87G>T	intron_variant
TUBB	NM_001293214.2 linkuse as main transcript	c.34+110G>T	intron_variant
TUBB	NR_120608.2 linkuse as main transcript	n.212+87G>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB	ENST00000327892.13 linkuse as main transcript	c.57+87G>T		intron_variant		1	NM_178014.4	P1
TUBB	ENST00000681435.1 linkuse as main transcript	c.-159-1887G>T		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39506

AN:

151938

Hom.:

6331

Cov.:

show subpopulations

Gnomad AFR

AF:

0.453

Gnomad AMI

AF:

0.174

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.178

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.266

Gnomad NFE

AF:

0.202

Gnomad OTH

AF:

0.266

GnomAD4 exome

AF:

0.200

AC:

200257

AN:

1003666

Hom.:

22705

AF XY:

0.197

AC XY:

101113

AN XY:

512236

show subpopulations

Gnomad4 AFR exome

AF:

0.461

Gnomad4 AMR exome

AF:

0.146

Gnomad4 ASJ exome

AF:

0.194

Gnomad4 EAS exome

AF:

0.193

Gnomad4 SAS exome

AF:

0.144

Gnomad4 FIN exome

AF:

0.109

Gnomad4 NFE exome

AF:

0.205

Gnomad4 OTH exome

AF:

0.212

GnomAD4 genome

AF:

0.260

AC:

39560

AN:

152056

Hom.:

6353

Cov.:

AF XY:

0.250

AC XY:

18610

AN XY:

74342

show subpopulations

Gnomad4 AFR

AF:

0.453

Gnomad4 AMR

AF:

0.187

Gnomad4 ASJ

AF:

0.187

Gnomad4 EAS

AF:

0.177

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.102

Gnomad4 NFE

AF:

0.202

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.210

Hom.:

3896

Bravo

AF:

0.276

Asia WGS

AF:

0.225

AC:

781

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 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

1.8

DANN

Benign

0.24

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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