16-89935117-C-T
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_006086.4(TUBB3):c.666C>T(p.Tyr222Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,614,164 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006086.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUBB3 | ENST00000315491.12 | c.666C>T | p.Tyr222Tyr | synonymous_variant | Exon 4 of 4 | 1 | NM_006086.4 | ENSP00000320295.7 | ||
ENSG00000198211 | ENST00000556922.1 | c.1707C>T | p.Tyr569Tyr | synonymous_variant | Exon 5 of 5 | 2 | ENSP00000451560.1 |
Frequencies
GnomAD3 genomes AF: 0.00117 AC: 178AN: 152222Hom.: 7 Cov.: 33
GnomAD3 exomes AF: 0.00417 AC: 1049AN: 251434Hom.: 30 AF XY: 0.00564 AC XY: 767AN XY: 135910
GnomAD4 exome AF: 0.00209 AC: 3062AN: 1461824Hom.: 65 Cov.: 31 AF XY: 0.00306 AC XY: 2226AN XY: 727210
GnomAD4 genome AF: 0.00116 AC: 176AN: 152340Hom.: 7 Cov.: 33 AF XY: 0.00148 AC XY: 110AN XY: 74496
ClinVar
Submissions by phenotype
not specified Benign:3
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not provided Benign:3
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TUBB3-related disorder Benign:1
This variant is classified as 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