16-29977794-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BS2
The NM_016151.4(TAOK2):c.22G>A(p.Gly8Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,614,036 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G8A) has been classified as Uncertain significance.
Frequency
Consequence
NM_016151.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAOK2 | NM_016151.4 | c.22G>A | p.Gly8Arg | missense_variant | 2/16 | ENST00000308893.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAOK2 | ENST00000308893.9 | c.22G>A | p.Gly8Arg | missense_variant | 2/16 | 1 | NM_016151.4 | ||
TAOK2 | ENST00000543033.5 | c.22G>A | p.Gly8Arg | missense_variant | 2/17 | 1 | |||
TAOK2 | ENST00000279394.7 | c.22G>A | p.Gly8Arg | missense_variant | 2/19 | 1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250904Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135780
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727230
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.22G>A (p.G8R) alteration is located in exon 2 (coding exon 1) of the TAOK2 gene. This alteration results from a G to A substitution at nucleotide position 22, causing the glycine (G) at amino acid position 8 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 8 of the TAOK2 protein (p.Gly8Arg). This variant is present in population databases (rs755972701, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with TAOK2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1919875). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at