17-29426600-G-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_020791.4(TAOK1):​c.-94-24855G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

TAOK1
NM_020791.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300
Variant links:
Genes affected
TAOK1 (HGNC:29259): (TAO kinase 1) Enables alpha-tubulin binding activity; beta-tubulin binding activity; and kinase activity. Involved in several processes, including mitotic G2 DNA damage checkpoint signaling; negative regulation of microtubule depolymerization; and positive regulation of JNK cascade. Located in microtubule cytoskeleton and perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TAOK1NM_020791.4 linkc.-94-24855G>T intron_variant Intron 1 of 19 ENST00000261716.8 NP_065842.1 Q7L7X3-1A0A024QZ70
TAOK1NM_025142.1 linkc.-94-24855G>T intron_variant Intron 1 of 17 NP_079418.1 Q7L7X3-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TAOK1ENST00000261716.8 linkc.-94-24855G>T intron_variant Intron 1 of 19 1 NM_020791.4 ENSP00000261716.3 Q7L7X3-1
TAOK1ENST00000536202.1 linkc.-94-24855G>T intron_variant Intron 1 of 17 1 ENSP00000438819.1 Q7L7X3-3
TAOK1ENST00000583121.5 linkc.-94-24855G>T intron_variant Intron 2 of 4 3 ENSP00000464562.1 J3QS76
TAOK1ENST00000587277.1 linkn.101-24855G>T intron_variant Intron 1 of 1 2

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
1.7
DANN
Benign
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6505129; hg19: chr17-27753618; API