rs17440433

Variant names:

• chr12-118201507-G-A
• rs17440433
• NM_016281.4:c.820-44C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-118201507-G-A
• chr12-118201507-G-C

Variant summary

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

The NM_016281.4(TAOK3):​c.820-44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,561,866 control chromosomes in the GnomAD database, including 13,614 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 0.10 (989 hom., cov: 32)
  • Exomes 𝑓: 0.13 (12625 hom.)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016281.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAOK3	NM_016281.4	MANE Select	c.820-44C>T		intron	N/A	NP_057365.3
	TAOK3	NM_001346487.2		c.820-44C>T		intron	N/A	NP_001333416.1
	TAOK3	NM_001346488.2		c.820-44C>T		intron	N/A	NP_001333417.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAOK3	ENST00000392533.8	TSL:1 MANE Select	c.820-44C>T		intron	N/A	ENSP00000376317.3
	TAOK3	ENST00000419821.6	TSL:1	c.820-44C>T		intron	N/A	ENSP00000416374.2
	TAOK3	ENST00000536584.1	TSL:1	n.156-44C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15414 AN: 152044 Hom.: 988 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.0904

GnomAD2 exomes AF: 0.106 AC: 24641 AN: 231444 AF XY: 0.109

Gnomad AFR exome AF: 0.0295

Gnomad AMR exome AF: 0.0697

Gnomad ASJ exome AF: 0.132

Gnomad EAS exome AF: 0.00333

Gnomad FIN exome AF: 0.158

Gnomad NFE exome AF: 0.144

Gnomad OTH exome AF: 0.127

GnomAD4 exome AF: 0.130 AC: 182898 AN: 1409704 Hom.: 12625 Cov.: 24 AF XY: 0.128 AC XY: 89842 AN XY: 699928

African (AFR) AF: 0.0304 AC: 971 AN: 31952

American (AMR) AF: 0.0723 AC: 2915 AN: 40330

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 3118 AN: 24176

East Asian (EAS) AF: 0.0280 AC: 1099 AN: 39196

South Asian (SAS) AF: 0.0584 AC: 4686 AN: 80240

European-Finnish (FIN) AF: 0.162 AC: 8441 AN: 51970

Middle Eastern (MID) AF: 0.116 AC: 641 AN: 5524

European-Non Finnish (NFE) AF: 0.143 AC: 154014 AN: 1078188

Other (OTH) AF: 0.121 AC: 7013 AN: 58128

GnomAD4 genome AF: 0.101 AC: 15410 AN: 152162 Hom.: 989 Cov.: 32 AF XY: 0.100 AC XY: 7437 AN XY: 74394

African (AFR) AF: 0.0326 AC: 1354 AN: 41542

American (AMR) AF: 0.0986 AC: 1506 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5172

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1723 AN: 10580

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9730 AN: 67998

Other (OTH) AF: 0.0913 AC: 192 AN: 2102

Alfa AF: 0.0906 Hom.: 211

Bravo AF: 0.0919

Asia WGS AF: 0.0290 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.82
PhyloP100		0.043
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs17440433; hg19: chr12-118639312;