Variant rs4713354 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000681435.1(TUBB):c.-160+4A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 152,232 control chromosomes in the GnomAD database, including 5,585 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.22 ( 5585 hom., cov: 33)

Exomes 𝑓: 0.19 ( 0 hom. )

Consequence

TUBB
ENST00000681435.1 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.970

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:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.30717643A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBB	ENST00000681435.1 linkuse as main transcript	c.-160+4A>C		splice_region_variant, intron_variant				ENSP00000506665.1		Q5ST81

Frequencies

GnomAD3 genomes

AF:

0.216

AC:

32830

AN:

152080

Hom.:

5565

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.0362

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.159

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.0403

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.101

Gnomad OTH

AF:

0.245

GnomAD4 exome

AF:

0.188

AC:

AN:

Hom.:

Cov.:

AF XY:

0.200

AC XY:

AN XY:

show subpopulations

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.150

Gnomad4 NFE exome

AF:

0.200

GnomAD4 genome

AF:

0.216

AC:

32890

AN:

152200

Hom.:

5585

Cov.:

AF XY:

0.212

AC XY:

15790

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.468

Gnomad4 AMR

AF:

0.207

Gnomad4 ASJ

AF:

0.159

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.188

Gnomad4 FIN

AF:

0.0403

Gnomad4 NFE

AF:

0.101

Gnomad4 OTH

AF:

0.247

Alfa

AF:

0.137

Hom.:

1650

Bravo

AF:

0.242

Asia WGS

AF:

0.243

AC:

845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.0

DANN

Benign

0.61

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over