chr17-59890897-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016261.4(TUBD1):c.106A>G(p.Met36Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M36L) has been classified as Uncertain significance.
Frequency
Consequence
NM_016261.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBD1 | NM_016261.4 | c.106A>G | p.Met36Val | missense_variant | 2/9 | ENST00000325752.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBD1 | ENST00000325752.8 | c.106A>G | p.Met36Val | missense_variant | 2/9 | 5 | NM_016261.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 251046Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135730
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461646Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727138
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.106A>G (p.M36V) alteration is located in exon 2 (coding exon 1) of the TUBD1 gene. This alteration results from a A to G substitution at nucleotide position 106, causing the methionine (M) at amino acid position 36 to be replaced by a valine (V). 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