rs199717430
Positions:
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
NM_006009.4 intron
Scores
2
13
Clinical Significance
Conservation
PhyloP100: 0.747
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]
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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 |
---|---|---|---|---|---|---|---|---|
TUBA1A | NM_006009.4 | c.226+10C>T | intron_variant | ENST00000301071.12 | NP_006000.2 | |||
TUBA1A | NM_001270399.2 | c.226+10C>T | intron_variant | NP_001257328.1 | ||||
TUBA1A | NM_001270400.2 | c.121+10C>T | intron_variant | NP_001257329.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBA1A | ENST00000301071.12 | c.226+10C>T | intron_variant | 1 | NM_006009.4 | ENSP00000301071.7 |
Frequencies
GnomAD3 genomes AF: 0.000854 AC: 130AN: 152158Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.000887 AC: 223AN: 251358Hom.: 0 AF XY: 0.000942 AC XY: 128AN XY: 135852
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GnomAD4 exome AF: 0.000709 AC: 1037AN: 1461718Hom.: 14 Cov.: 38 AF XY: 0.000734 AC XY: 534AN XY: 727158
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GnomAD4 genome AF: 0.000841 AC: 128AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.000994 AC XY: 74AN XY: 74452
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | TUBA1A: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Feb 14, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 28, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 23, 2015 | - - |
TUBA1A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2020 | This 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:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
T
Vest4
MVP
ClinPred
T
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at