12-49185913-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_006009.4(TUBA1A):c.453G>A(p.Ser151Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,538 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S151S) has been classified as Benign.
Frequency
Consequence
NM_006009.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TUBA1A | NM_006009.4 | c.453G>A | p.Ser151Ser | synonymous_variant | 4/4 | ENST00000301071.12 | NP_006000.2 | |
TUBA1A | NM_001270399.2 | c.453G>A | p.Ser151Ser | synonymous_variant | 4/4 | NP_001257328.1 | ||
TUBA1A | NM_001270400.2 | c.348G>A | p.Ser116Ser | synonymous_variant | 4/4 | NP_001257329.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBA1A | ENST00000301071.12 | c.453G>A | p.Ser151Ser | synonymous_variant | 4/4 | 1 | NM_006009.4 | ENSP00000301071.7 |
Frequencies
GnomAD3 genomes Cov.: 30
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250668Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135530
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461538Hom.: 0 Cov.: 76 AF XY: 0.0000110 AC XY: 8AN XY: 727072
GnomAD4 genome Cov.: 30
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 19, 2023 | - - |
TUBA1A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2019 | 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at