Variant chr12-49128795-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006082.3(TUBA1B):c.519A>G(p.Pro173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 1,487,486 control chromosomes in the GnomAD database, including 123,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.44 ( 16481 hom., cov: 28)

Exomes 𝑓: 0.36 ( 107409 hom. )

Consequence

TUBA1B
NM_006082.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.21

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-AS1 (HGNC:56356): (TUBA1B antisense RNA 1)

TUBA1B-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.64).

BP6

Variant 12-49128795-T-C is Benign according to our data. Variant chr12-49128795-T-C is described in ClinVar as [Benign]. Clinvar id is 768541.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBA1B	NM_006082.3 linkuse as main transcript	c.519A>G	p.Pro173=	synonymous_variant	4/4	ENST00000336023.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBA1B	ENST00000336023.9 linkuse as main transcript	c.519A>G	p.Pro173=	synonymous_variant	4/4	1	NM_006082.3	P1	P68363-1

Frequencies

GnomAD3 genomes

AF:

0.445

AC:

67015

AN:

150740

Hom.:

16438

Cov.:

show subpopulations

Gnomad AFR

AF:

0.640

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.365

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.713

Gnomad SAS

AF:

0.556

Gnomad FIN

AF:

0.384

Gnomad MID

AF:

0.263

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.411

GnomAD3 exomes

AF:

0.365

AC:

71414

AN:

195902

Hom.:

21446

AF XY:

0.364

AC XY:

38019

AN XY:

104356

show subpopulations

Gnomad AFR exome

AF:

0.634

Gnomad AMR exome

AF:

0.294

Gnomad ASJ exome

AF:

0.200

Gnomad EAS exome

AF:

0.757

Gnomad SAS exome

AF:

0.529

Gnomad FIN exome

AF:

0.346

Gnomad NFE exome

AF:

0.258

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

AF:

0.361

AC:

482330

AN:

1336628

Hom.:

107409

Cov.:

AF XY:

0.364

AC XY:

242104

AN XY:

665034

show subpopulations

Gnomad4 AFR exome

AF:

0.660

Gnomad4 AMR exome

AF:

0.329

Gnomad4 ASJ exome

AF:

0.261

Gnomad4 EAS exome

AF:

0.721

Gnomad4 SAS exome

AF:

0.530

Gnomad4 FIN exome

AF:

0.378

Gnomad4 NFE exome

AF:

0.327

Gnomad4 OTH exome

AF:

0.379

GnomAD4 genome

AF:

0.445

AC:

67117

AN:

150858

Hom.:

16481

Cov.:

AF XY:

0.448

AC XY:

33013

AN XY:

73648

show subpopulations

Gnomad4 AFR

AF:

0.640

Gnomad4 AMR

AF:

0.365

Gnomad4 ASJ

AF:

0.270

Gnomad4 EAS

AF:

0.714

Gnomad4 SAS

AF:

0.555

Gnomad4 FIN

AF:

0.384

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.410

Alfa

AF:

0.359

Hom.:

1889

Bravo

AF:

0.449

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 27, 2020	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.64

CADD

Benign

7.1

DANN

Benign

0.56

RBP_binding_hub_radar

0.92

RBP_regulation_power_radar

2.8

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