Variant chr18-12308274-G-T 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.-19G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,432,188 control chromosomes in the GnomAD database, including 8,785 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 928 hom., cov: 33)

Exomes 𝑓: 0.11 ( 7857 hom. )

Consequence

TUBB6
NM_032525.3 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.00900

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 18-12308274-G-T is Benign according to our data. Variant chr18-12308274-G-T is described in ClinVar as [Benign]. Clinvar id is 1684207.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.152 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.-19G>T		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.-19G>T		5_prime_UTR_variant	1/4	1	NM_032525.3	P1

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16479

AN:

150672

Hom.:

929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0821

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.160

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0831

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.111

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.119

AC:

15108

AN:

127258

Hom.:

942

AF XY:

0.118

AC XY:

8557

AN XY:

72418

show subpopulations

Gnomad AFR exome

AF:

0.0773

Gnomad AMR exome

AF:

0.164

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.141

Gnomad SAS exome

AF:

0.113

Gnomad FIN exome

AF:

0.0836

Gnomad NFE exome

AF:

0.106

Gnomad OTH exome

AF:

0.140

GnomAD4 exome

AF:

0.107

AC:

137306

AN:

1281408

Hom.:

7857

Cov.:

AF XY:

0.109

AC XY:

68903

AN XY:

634702

show subpopulations

Gnomad4 AFR exome

AF:

0.0772

Gnomad4 AMR exome

AF:

0.161

Gnomad4 ASJ exome

AF:

0.155

Gnomad4 EAS exome

AF:

0.183

Gnomad4 SAS exome

AF:

0.115

Gnomad4 FIN exome

AF:

0.0908

Gnomad4 NFE exome

AF:

0.103

Gnomad4 OTH exome

AF:

0.114

GnomAD4 genome

AF:

0.109

AC:

16478

AN:

150780

Hom.:

928

Cov.:

AF XY:

0.110

AC XY:

8070

AN XY:

73648

show subpopulations

Gnomad4 AFR

AF:

0.0820

Gnomad4 AMR

AF:

0.157

Gnomad4 ASJ

AF:

0.157

Gnomad4 EAS

AF:

0.159

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0831

Gnomad4 NFE

AF:

0.111

Gnomad4 OTH

AF:

0.129

Alfa

AF:

0.0455

Hom.:

Bravo

AF:

0.113

Asia WGS

AF:

0.130

AC:

424

AN:

3244

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

DANN

Benign

0.71

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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