rs2234331

Positions:

chr22-18126361-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_018943.3(TUBA8):c.383C>T(p.Ala128Val) variant causes a missense change. The variant allele was found at a frequency of 0.0108 in 1,614,118 control chromosomes in the GnomAD database, including 128 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0075 ( 9 hom., cov: 32)

Exomes 𝑓: 0.011 ( 119 hom. )

Consequence

TUBA8
NM_018943.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 5.26

Variant links:

Genes affected

TUBA8 (HGNC:12410): (tubulin alpha 8) This gene encodes a member of the alpha tubulin protein family. Alpha tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form microtubules. Mutations in this gene are associated with polymicrogyria and optic nerve hypoplasia. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2010]

TUBA8 links:

ENSG00000288683 (HGNC:):

ENSG00000288683 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant 22-18126361-C-T is Benign according to our data. Variant chr22-18126361-C-T is described in ClinVar as [Benign]. Clinvar id is 160173.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-18126361-C-T is described in Lovd as [Benign].

BS2

High Homozygotes in GnomAd4 at 9 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBA8	NM_018943.3 linkuse as main transcript	c.383C>T	p.Ala128Val	missense_variant	4/5	ENST00000330423.8	NP_061816.1	Q9NY65-1
TUBA8	NM_001193414.2 linkuse as main transcript	c.185C>T	p.Ala62Val	missense_variant	4/5		NP_001180343.1	Q9NY65-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TUBA8	ENST00000330423.8 linkuse as main transcript	c.383C>T	p.Ala128Val	missense_variant	4/5	1	NM_018943.3	ENSP00000333326.3	Q9NY65-1
ENSG00000288683	ENST00000474897.6 linkuse as main transcript	n.*273C>T		non_coding_transcript_exon_variant	8/9	5		ENSP00000434235.2	E9PRC5
ENSG00000288683	ENST00000474897.6 linkuse as main transcript	n.*273C>T		3_prime_UTR_variant	8/9	5		ENSP00000434235.2	E9PRC5

Frequencies

GnomAD3 genomes

AF:

0.00750

AC:

1141

AN:

152184

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00278

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00373

Gnomad ASJ

AF:

0.00173

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00559

Gnomad FIN

AF:

0.00480

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0128

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00709

AC:

1780

AN:

251010

Hom.:

AF XY:

0.00733

AC XY:

995

AN XY:

135800

show subpopulations

Gnomad AFR exome

AF:

0.00248

Gnomad AMR exome

AF:

0.00263

Gnomad ASJ exome

AF:

0.00298

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00536

Gnomad FIN exome

AF:

0.00439

Gnomad NFE exome

AF:

0.0116

Gnomad OTH exome

AF:

0.00686

GnomAD4 exome

AF:

0.0111

AC:

16251

AN:

1461816

Hom.:

119

Cov.:

AF XY:

0.0109

AC XY:

7936

AN XY:

727208

show subpopulations

Gnomad4 AFR exome

AF:

0.00227

Gnomad4 AMR exome

AF:

0.00271

Gnomad4 ASJ exome

AF:

0.00214

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00616

Gnomad4 FIN exome

AF:

0.00470

Gnomad4 NFE exome

AF:

0.0131

Gnomad4 OTH exome

AF:

0.00979

GnomAD4 genome

AF:

0.00749

AC:

1140

AN:

152302

Hom.:

Cov.:

AF XY:

0.00698

AC XY:

520

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.00277

Gnomad4 AMR

AF:

0.00373

Gnomad4 ASJ

AF:

0.00173

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00539

Gnomad4 FIN

AF:

0.00480

Gnomad4 NFE

AF:

0.0128

Gnomad4 OTH

AF:

0.00615

Alfa

AF:

0.0107

Hom.:

Bravo

AF:

0.00724

TwinsUK

AF:

0.0140

AC:

ALSPAC

AF:

0.0138

AC:

ESP6500AA

AF:

0.00318

AC:

ESP6500EA

AF:

0.0113

AC:

ExAC

AF:

0.00699

AC:

849

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.0103

EpiControl

AF:

0.0125

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 16, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2024	ENSG00000280007: BS1, BS2; TUBA8: BS1, BS2 -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 02, 2017	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 23, 2013	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.32

BayesDel_noAF

Benign

-0.22

CADD

Uncertain

DANN

Benign

0.97

DEOGEN2

Benign

0.23

.;T;T

Eigen

Benign

0.16

Eigen_PC

Uncertain

0.30

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.95

D;D;D

MetaRNN

Benign

0.015

T;T;T

MetaSVM

Benign

-0.64

MutationAssessor

Benign

1.6

.;L;.

PrimateAI

Uncertain

0.62

PROVEAN

Benign

-0.68

N;N;N

REVEL

Benign

0.16

Sift

Uncertain

0.0050

.;D;D

Sift4G

Benign

0.091

T;T;T

Polyphen

0.039, 0.22

.;B;B

Vest4

0.47

MVP

0.89

MPC

0.27

ClinPred

0.020

GERP RS

5.5

Varity_R

0.12

gMVP

0.29

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.27

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.27

Position offset: 17

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