rs17440336

Variant names:

• chr12-118163305-C-T
• rs17440336
• NM_016281.4:c.1900-1278G>A

Variant summary

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

The NM_016281.4(TAOK3):​c.1900-1278G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,176 control chromosomes in the GnomAD database, including 1,201 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 0.12 (1201 hom., cov: 32)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 2 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAOK3	NM_016281.4	c.1900-1278G>A		intron_variant	Intron 17 of 20	ENST00000392533.8	NP_057365.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAOK3	ENST00000392533.8	c.1900-1278G>A		intron_variant	Intron 17 of 20	1	NM_016281.4	ENSP00000376317.3
TAOK3	ENST00000419821.6	c.1900-1278G>A		intron_variant	Intron 17 of 20	1		ENSP00000416374.2
TAOK3	ENST00000537952.1	c.520-1278G>A		intron_variant	Intron 4 of 7	2		ENSP00000443834.1
TAOK3	ENST00000537305.5	n.2581-1278G>A		intron_variant	Intron 14 of 17	5

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18317 AN: 152058 Hom.: 1200 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0579

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.120 AC: 18319 AN: 152176 Hom.: 1201 Cov.: 32 AF XY: 0.118 AC XY: 8813 AN XY: 74386

African (AFR) AF: 0.0997 AC: 4138 AN: 41510

American (AMR) AF: 0.104 AC: 1589 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 469 AN: 3470

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5186

South Asian (SAS) AF: 0.0588 AC: 284 AN: 4828

European-Finnish (FIN) AF: 0.166 AC: 1751 AN: 10578

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9709 AN: 68006

Other (OTH) AF: 0.105 AC: 222 AN: 2106

Alfa AF: 0.133 Hom.: 617

Bravo AF: 0.113

Asia WGS AF: 0.0370 AC: 129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.65
PhyloP100		0.29
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: rs17440336; hg19: chr12-118601110;