12-118172488-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_016281.4(TAOK3):c.1868G>A(p.Arg623Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,948 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016281.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TAOK3 | ENST00000392533.8 | c.1868G>A | p.Arg623Gln | missense_variant | Exon 17 of 21 | 1 | NM_016281.4 | ENSP00000376317.3 | ||
TAOK3 | ENST00000419821.6 | c.1868G>A | p.Arg623Gln | missense_variant | Exon 17 of 21 | 1 | ENSP00000416374.2 | |||
TAOK3 | ENST00000537952.1 | c.488G>A | p.Arg163Gln | missense_variant | Exon 4 of 8 | 2 | ENSP00000443834.1 | |||
TAOK3 | ENST00000537305.5 | n.2549G>A | non_coding_transcript_exon_variant | Exon 14 of 18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251466Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135904
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727236
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1868G>A (p.R623Q) alteration is located in exon 17 (coding exon 15) of the TAOK3 gene. This alteration results from a G to A substitution at nucleotide position 1868, causing the arginine (R) at amino acid position 623 to be replaced by a glutamine (Q). 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