chr12-49185913-C-T
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2
The NM_006009.4(TUBA1A):c.453G>A(p.Ser151=) 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 -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBA1A | NM_006009.4 | c.453G>A | p.Ser151= | synonymous_variant | 4/4 | ENST00000301071.12 | |
TUBA1A | NM_001270399.2 | c.453G>A | p.Ser151= | synonymous_variant | 4/4 | ||
TUBA1A | NM_001270400.2 | c.348G>A | p.Ser116= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBA1A | ENST00000301071.12 | c.453G>A | p.Ser151= | synonymous_variant | 4/4 | 1 | NM_006009.4 | P1 | |
TUBA1B-AS1 | ENST00000656133.1 | n.474-2370C>T | intron_variant, non_coding_transcript_variant |
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 | Invitae | Nov 19, 2023 | - - |
TUBA1A-related disorder Benign:1
Likely benign, criteria provided, single submitter | 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