Variant chr18-12308244-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032525.3(TUBB6):c.-49T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,335,354 control chromosomes in the GnomAD database, including 395,444 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.67 ( 35120 hom., cov: 32)

Exomes 𝑓: 0.78 ( 360324 hom. )

Consequence

TUBB6
NM_032525.3 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.481

Variant links:

Genes affected

TUBB6 (HGNC:20776): (tubulin beta 6 class V) Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization and mitotic cell cycle. Located in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

TUBB6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 18-12308244-T-A is Benign according to our data. Variant chr18-12308244-T-A is described in ClinVar as [Benign]. Clinvar id is 1684204.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBB6	NM_032525.3 linkuse as main transcript	c.-49T>A		5_prime_UTR_variant	1/4	ENST00000317702.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB6	ENST00000317702.10 linkuse as main transcript	c.-49T>A		5_prime_UTR_variant	1/4	1	NM_032525.3	P1

Frequencies

GnomAD3 genomes

AF:

0.673

AC:

100035

AN:

148630

Hom.:

35109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.467

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.629

Gnomad ASJ

AF:

0.743

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.771

Gnomad FIN

AF:

0.816

Gnomad MID

AF:

0.725

Gnomad NFE

AF:

0.782

Gnomad OTH

AF:

0.673

GnomAD3 exomes

AF:

0.749

AC:

61364

AN:

81930

Hom.:

23358

AF XY:

0.760

AC XY:

35996

AN XY:

47370

show subpopulations

Gnomad AFR exome

AF:

0.487

Gnomad AMR exome

AF:

0.592

Gnomad ASJ exome

AF:

0.748

Gnomad EAS exome

AF:

0.652

Gnomad SAS exome

AF:

0.789

Gnomad FIN exome

AF:

0.821

Gnomad NFE exome

AF:

0.804

Gnomad OTH exome

AF:

0.740

GnomAD4 exome

AF:

0.776

AC:

921169

AN:

1186616

Hom.:

360324

Cov.:

AF XY:

0.777

AC XY:

453593

AN XY:

583814

show subpopulations

Gnomad4 AFR exome

AF:

0.467

Gnomad4 AMR exome

AF:

0.605

Gnomad4 ASJ exome

AF:

0.755

Gnomad4 EAS exome

AF:

0.607

Gnomad4 SAS exome

AF:

0.782

Gnomad4 FIN exome

AF:

0.814

Gnomad4 NFE exome

AF:

0.792

Gnomad4 OTH exome

AF:

0.753

GnomAD4 genome

AF:

0.673

AC:

100064

AN:

148738

Hom.:

35120

Cov.:

AF XY:

0.674

AC XY:

48894

AN XY:

72508

show subpopulations

Gnomad4 AFR

AF:

0.467

Gnomad4 AMR

AF:

0.629

Gnomad4 ASJ

AF:

0.743

Gnomad4 EAS

AF:

0.607

Gnomad4 SAS

AF:

0.772

Gnomad4 FIN

AF:

0.816

Gnomad4 NFE

AF:

0.782

Gnomad4 OTH

AF:

0.675

Alfa

AF:

0.653

Hom.:

2272

Bravo

AF:

0.651

Asia WGS

AF:

0.653

AC:

2042

AN:

3130

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Facial palsy, congenital, with ptosis and velopharyngeal dysfunction

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Dec 05, 2021

- -

not provided

Benign:1

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

-0.75

CADD

Benign

6.7

DANN

Benign

0.64

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