rs199717430

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_006009.4(TUBA1A):​c.226+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000722 in 1,613,994 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.00084 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00071 ( 14 hom. )

Consequence

TUBA1A
NM_006009.4 intron

Scores

2
13

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.747
Variant links:
Genes affected
TUBA1A (HGNC:20766): (tubulin alpha 1a) Microtubules of the eukaryotic cytoskeleton perform essential and diverse functions and are composed of a heterodimer of alpha and beta tubulins. The genes encoding these microtubule constituents belong to the tubulin superfamily, which is composed of six distinct families. Genes from the alpha, beta and gamma tubulin families are found in all eukaryotes. The alpha and beta tubulins represent the major components of microtubules, while gamma tubulin plays a critical role in the nucleation of microtubule assembly. There are multiple alpha and beta tubulin genes, which are highly conserved among species. This gene encodes alpha tubulin and is highly similar to the mouse and rat Tuba1 genes. Northern blot studies have shown that the gene expression is predominantly found in morphologically differentiated neurologic cells. This gene is one of three alpha-tubulin genes in a cluster on chromosome 12q. Mutations in this gene cause lissencephaly type 3 (LIS3) - a neurological condition characterized by microcephaly, intellectual disability, and early-onset epilepsy caused by defective neuronal migration. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]

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 (MetaRNN=0.005897194).
BP6
Variant 12-49186601-G-A is Benign according to our data. Variant chr12-49186601-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 160152.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-49186601-G-A is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000709 (1037/1461718) while in subpopulation MID AF= 0.0347 (200/5768). AF 95% confidence interval is 0.0307. There are 14 homozygotes in gnomad4_exome. There are 534 alleles in male gnomad4_exome subpopulation. Median coverage is 38. This position pass quality control queck.
BS2
High AC in GnomAd4 at 128 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TUBA1ANM_006009.4 linkuse as main transcriptc.226+10C>T intron_variant ENST00000301071.12 NP_006000.2 Q71U36-1
TUBA1ANM_001270399.2 linkuse as main transcriptc.226+10C>T intron_variant NP_001257328.1 Q71U36-1
TUBA1ANM_001270400.2 linkuse as main transcriptc.121+10C>T intron_variant NP_001257329.1 Q71U36-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TUBA1AENST00000301071.12 linkuse as main transcriptc.226+10C>T intron_variant 1 NM_006009.4 ENSP00000301071.7 Q71U36-1

Frequencies

GnomAD3 genomes
AF:
0.000854
AC:
130
AN:
152158
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000786
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00405
Gnomad MID
AF:
0.0348
Gnomad NFE
AF:
0.000720
Gnomad OTH
AF:
0.000957
GnomAD3 exomes
AF:
0.000887
AC:
223
AN:
251358
Hom.:
0
AF XY:
0.000942
AC XY:
128
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000549
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000555
Gnomad FIN exome
AF:
0.00379
Gnomad NFE exome
AF:
0.000800
Gnomad OTH exome
AF:
0.00228
GnomAD4 exome
AF:
0.000709
AC:
1037
AN:
1461718
Hom.:
14
Cov.:
38
AF XY:
0.000734
AC XY:
534
AN XY:
727158
show subpopulations
Gnomad4 AFR exome
AF:
0.000358
Gnomad4 AMR exome
AF:
0.000604
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000638
Gnomad4 FIN exome
AF:
0.00367
Gnomad4 NFE exome
AF:
0.000430
Gnomad4 OTH exome
AF:
0.00113
GnomAD4 genome
AF:
0.000841
AC:
128
AN:
152276
Hom.:
1
Cov.:
32
AF XY:
0.000994
AC XY:
74
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.000785
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.00405
Gnomad4 NFE
AF:
0.000720
Gnomad4 OTH
AF:
0.000947
Alfa
AF:
0.00100
Hom.:
0
Bravo
AF:
0.000555
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000582
AC:
5
ExAC
AF:
0.000708
AC:
86
EpiCase
AF:
0.00104
EpiControl
AF:
0.00172

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:5
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMar 01, 2022TUBA1A: BS1, BS2 -
Benign, criteria provided, single submitterclinical testingAthena DiagnosticsFeb 14, 2018- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 30, 2024- -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Likely benign, criteria provided, single submitterclinical testingGeneDxMar 28, 2018- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoAug 23, 2015- -
TUBA1A-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMar 12, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
14
DANN
Benign
0.90
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.40
FATHMM_MKL
Benign
0.076
N
LIST_S2
Benign
0.22
T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.0059
T
MetaSVM
Benign
-0.71
T
PROVEAN
Benign
-1.0
N
REVEL
Benign
0.055
Sift
Uncertain
0.0070
D
Sift4G
Uncertain
0.058
T
Vest4
0.12
MVP
0.56
ClinPred
0.031
T
GERP RS
3.0

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.

Other links and lift over

dbSNP: rs199717430; hg19: chr12-49580384; API