Variant chr12-49128822-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_006082.3(TUBA1B):c.492G>A(p.Lys164Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 1,589,318 control chromosomes in the GnomAD database, including 78,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10048 hom., cov: 30)

Exomes 𝑓: 0.34 ( 68764 hom. )

Consequence

TUBA1B
NM_006082.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.61

Variant links:

Genes affected

TUBA1B (HGNC:18809): (tubulin alpha 1b) Enables double-stranded RNA binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Predicted to act upstream of or within cellular response to interleukin-4. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TUBA1B links:

TUBA1B (HGNC:):

TUBA1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 12-49128822-C-T is Benign according to our data. Variant chr12-49128822-C-T is described in ClinVar as [Benign]. Clinvar id is 1236526.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=2.61 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBA1B	NM_006082.3 linkuse as main transcript	c.492G>A	p.Lys164Lys	synonymous_variant	4/4	ENST00000336023.9	NP_006073.2	P68363-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBA1B	ENST00000336023.9 linkuse as main transcript	c.492G>A	p.Lys164Lys	synonymous_variant	4/4	1	NM_006082.3	ENSP00000336799.5		P68363-1

Frequencies

GnomAD3 genomes

AF:

0.355

AC:

53780

AN:

151292

Hom.:

10049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.342

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.328

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.547

Gnomad FIN

AF:

0.381

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.341

GnomAD3 exomes

AF:

0.356

AC:

85811

AN:

240850

Hom.:

14379

AF XY:

0.361

AC XY:

46936

AN XY:

129878

show subpopulations

Gnomad AFR exome

AF:

0.315

Gnomad AMR exome

AF:

0.314

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.685

Gnomad SAS exome

AF:

0.477

Gnomad FIN exome

AF:

0.360

Gnomad NFE exome

AF:

0.302

Gnomad OTH exome

AF:

0.337

GnomAD4 exome

AF:

0.336

AC:

482453

AN:

1437908

Hom.:

68764

Cov.:

AF XY:

0.340

AC XY:

243308

AN XY:

715188

show subpopulations

Gnomad4 AFR exome

AF:

0.317

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.259

Gnomad4 EAS exome

AF:

0.691

Gnomad4 SAS exome

AF:

0.490

Gnomad4 FIN exome

AF:

0.375

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.342

GnomAD4 genome

AF:

0.355

AC:

53796

AN:

151410

Hom.:

10048

Cov.:

AF XY:

0.362

AC XY:

26787

AN XY:

73924

show subpopulations

Gnomad4 AFR

AF:

0.342

Gnomad4 AMR

AF:

0.328

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.713

Gnomad4 SAS

AF:

0.547

Gnomad4 FIN

AF:

0.381

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.339

Alfa

AF:

0.323

Hom.:

2094

Bravo

AF:

0.348

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 27, 2020	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.7

DANN

Benign

0.90

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