10-5393840-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024803.3(TUBAL3):c.1018G>A(p.Ala340Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000255 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024803.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBAL3 | ENST00000380419.8 | c.1018G>A | p.Ala340Thr | missense_variant | Exon 4 of 4 | 1 | NM_024803.3 | ENSP00000369784.3 | ||
TUBAL3 | ENST00000479328.1 | c.898G>A | p.Ala300Thr | missense_variant | Exon 4 of 4 | 1 | ENSP00000418799.1 |
Frequencies
GnomAD3 genomes AF: 0.000355 AC: 54AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000398 AC: 100AN: 251450Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135894
GnomAD4 exome AF: 0.000245 AC: 358AN: 1461852Hom.: 0 Cov.: 29 AF XY: 0.000235 AC XY: 171AN XY: 727226
GnomAD4 genome AF: 0.000355 AC: 54AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000497 AC XY: 37AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1018G>A (p.A340T) alteration is located in exon 4 (coding exon 4) of the TUBAL3 gene. This alteration results from a G to A substitution at nucleotide position 1018, causing the alanine (A) at amino acid position 340 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at