12-118181610-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_016281.4(TAOK3):c.1330-3C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00275 in 1,613,398 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 8 hom. )
Consequence
TAOK3
NM_016281.4 splice_region, splice_polypyrimidine_tract, intron
NM_016281.4 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.04630
2
Clinical Significance
Conservation
PhyloP100: 3.81
Genes affected
TAOK3 (HGNC:18133): (TAO kinase 3) The protein encoded by this gene is a serine/threonine protein kinase that activates the p38/MAPK14 stress-activated MAPK cascade but inhibits the basal activity of the MAPK8/JNK cascade. The encoded protein is a member of the GCK subfamily of STE20-like kinases. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 12-118181610-G-A is Benign according to our data. Variant chr12-118181610-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 784674.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 366 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TAOK3 | NM_016281.4 | c.1330-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000392533.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TAOK3 | ENST00000392533.8 | c.1330-3C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016281.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00240 AC: 366AN: 152188Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00232 AC: 582AN: 251074Hom.: 0 AF XY: 0.00226 AC XY: 306AN XY: 135692
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GnomAD4 exome AF: 0.00279 AC: 4070AN: 1461092Hom.: 8 Cov.: 31 AF XY: 0.00268 AC XY: 1946AN XY: 726824
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GnomAD4 genome AF: 0.00240 AC: 366AN: 152306Hom.: 2 Cov.: 32 AF XY: 0.00244 AC XY: 182AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at