rs9900280

Positions:

• chr17-29442580-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-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/exons	MANE	UniProt
TAOK1	NM_020791.4	c.-94-8875G>A		intron_variant		ENST00000261716.8
TAOK1	NM_025142.1	c.-94-8875G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAOK1	ENST00000261716.8	c.-94-8875G>A		intron_variant		1	NM_020791.4	P1
TAOK1	ENST00000536202.1	c.-94-8875G>A		intron_variant		1
TAOK1	ENST00000583121.5	c.-94-8875G>A		intron_variant		3
TAOK1	ENST00000587277.1	n.101-8875G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.553

Alfa AF: 0.532 Hom.: 43514

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

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: rs9900280; hg19: chr17-27769598;