rs571113

Positions:

• chr12-118355613-A-G

Variant summary

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

The NM_016281.4(TAOK3):​c.-194+17035T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 152,100 control chromosomes in the GnomAD database, including 13,958 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 0.42 (13958 hom., cov: 32)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TAOK3	NM_016281.4	c.-194+17035T>C		intron_variant		ENST00000392533.8	NP_057365.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TAOK3	ENST00000392533.8	c.-194+17035T>C		intron_variant		1	NM_016281.4	ENSP00000376317	P1

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63251 AN: 151982 Hom.: 13948 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.416 AC: 63278 AN: 152100 Hom.: 13958 Cov.: 32 AF XY: 0.419 AC XY: 31132 AN XY: 74346

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.420

Alfa AF: 0.466 Hom.: 34377

Bravo AF: 0.412

Asia WGS AF: 0.412 AC: 1436 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.55

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: rs571113; hg19: chr12-118793418;