Genetic Variant TAOK3:c.820-44C>T (chr12-118201507-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0430

Publications

6 publications found

Variant links:

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]

TAOK3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
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.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.128

AC XY:

89842

AN XY:

699928

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

7426

14852

22279

29705

37131

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5394

10788

16182

21576

26970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.101

AC:

15410

AN:

152162

Hom.:

989

Cov.:

AF XY:

0.100

AC XY:

7437

AN XY:

74394

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.143

AC:

9730

AN:

67998

Other (OTH)

AF:

0.0913

AC:

192

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

692

1384

2075

2767

3459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

344

516

688

860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0906

Hom.:

211

Bravo

AF:

0.0919

Asia WGS

AF:

0.0290

AC:

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

(source)

DANN

Benign

0.82

PhyloP100

0.043

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over