rs6505129

chr17-29426600-G-Achr17-29426600-G-Cchr17-29426600-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020791.4(TAOK1):c.-94-24855G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,074 control chromosomes in the GnomAD database, including 33,566 homozygotes. 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: 𝑓 0.65 (33566 hom., cov: 31)
• Consequence: TAOK1 NM_020791.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0300

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAOK1	NM_020791.4	c.-94-24855G>A		intron_variant		ENST00000261716.8
TAOK1	NM_025142.1	c.-94-24855G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAOK1	ENST00000261716.8	c.-94-24855G>A		intron_variant		1	NM_020791.4	P1
TAOK1	ENST00000536202.1	c.-94-24855G>A		intron_variant		1
TAOK1	ENST00000583121.5	c.-94-24855G>A		intron_variant		3
TAOK1	ENST00000587277.1	n.101-24855G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98063 AN: 151958 Hom.: 33513 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.592

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.646 AC: 98166 AN: 152074 Hom.: 33566 Cov.: 31 AF XY: 0.649 AC XY: 48243 AN XY: 74306

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.597

Alfa AF: 0.540 Hom.: 29289

Bravo AF: 0.658

Asia WGS AF: 0.828 AC: 2882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.0
Dann	Benign	0.45

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

Other links and lift over

dbSNP: rs6505129; hg19: chr17-27753618;