17-29442580-G-A

Variant names:

• chr17-29442580-G-A
• rs9900280
• NM_020791.4:c.-94-8875G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020791.4(TAOK1):​c.-94-8875G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.584 in 151,718 control chromosomes in the GnomAD database, including 26,476 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 0.58 (26476 hom., cov: 30)
• Consequence: TAOK1 NM_020791.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 24 publications found

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]

TAOK1 Gene-Disease associations (from GenCC):

• developmental delay with or without intellectual impairment or behavioral abnormalities

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• syndromic intellectual disability

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• complex neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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 rank	MANE	Protein	UniProt
TAOK1	NM_020791.4	c.-94-8875G>A		intron_variant	Intron 1 of 19	ENST00000261716.8	NP_065842.1
TAOK1	NM_025142.1	c.-94-8875G>A		intron_variant	Intron 1 of 17		NP_079418.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAOK1	ENST00000261716.8	c.-94-8875G>A		intron_variant	Intron 1 of 19	1	NM_020791.4	ENSP00000261716.3
TAOK1	ENST00000536202.1	c.-94-8875G>A		intron_variant	Intron 1 of 17	1		ENSP00000438819.1
TAOK1	ENST00000583121.5	c.-94-8875G>A		intron_variant	Intron 2 of 4	3		ENSP00000464562.1
TAOK1	ENST00000587277.1	n.101-8875G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88458 AN: 151602 Hom.: 26448 Cov.: 30

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.584 AC: 88536 AN: 151718 Hom.: 26476 Cov.: 30 AF XY: 0.590 AC XY: 43742 AN XY: 74126

African (AFR) AF: 0.644 AC: 26610 AN: 41348

American (AMR) AF: 0.578 AC: 8819 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1922 AN: 3470

East Asian (EAS) AF: 0.969 AC: 5012 AN: 5174

South Asian (SAS) AF: 0.649 AC: 3120 AN: 4806

European-Finnish (FIN) AF: 0.554 AC: 5788 AN: 10452

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.522 AC: 35461 AN: 67912

Other (OTH) AF: 0.553 AC: 1164 AN: 2104

Alfa AF: 0.540 Hom.: 71030

Bravo AF: 0.587

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.86
DANN	Benign	0.18
PhyloP100		0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9900280; hg19: chr17-27769598;