6-3153911-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001069.3(TUBB2A):c.1290C>T(p.Ala430=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000725 in 1,613,058 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. A430A) has been classified as Likely benign.
Frequency
Consequence
NM_001069.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB2A | NM_001069.3 | c.1290C>T | p.Ala430= | synonymous_variant | 4/4 | ENST00000333628.4 | |
TUBB2A | NM_001310315.2 | c.1035C>T | p.Ala345= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB2A | ENST00000333628.4 | c.1290C>T | p.Ala430= | synonymous_variant | 4/4 | 1 | NM_001069.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000396 AC: 6AN: 151676Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251164Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135750
GnomAD4 exome AF: 0.0000760 AC: 111AN: 1461382Hom.: 0 Cov.: 31 AF XY: 0.0000757 AC XY: 55AN XY: 726990
GnomAD4 genome ? AF: 0.0000396 AC: 6AN: 151676Hom.: 0 Cov.: 30 AF XY: 0.0000270 AC XY: 2AN XY: 74050
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at