Genetic Variant NM_016151.4:c.-35-118A>G (chr16-29977620-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_016151.4(TAOK2):c.-35-118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 964,436 control chromosomes in the GnomAD database, including 91,467 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 0.36 ( 10834 hom., cov: 31)

Exomes 𝑓: 0.44 ( 80633 hom. )

Consequence

TAOK2
NM_016151.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.18

Publications

18 publications found

Variant links:

Genes affected

TAOK2 (HGNC:16835): (TAO kinase 2) Enables mitogen-activated protein kinase kinase binding activity; neuropilin binding activity; and protein serine/threonine kinase activity. Involved in several processes, including focal adhesion assembly; intracellular signal transduction; and positive regulation of JNK cascade. Located in cytoplasmic vesicle; cytosol; and nuclear lumen. Part of receptor complex. [provided by Alliance of Genome Resources, Apr 2022]

TAOK2 Gene-Disease associations (from GenCC):

autism spectrum disorder
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
immunodeficiency disease
Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

TAOK2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAOK2	NM_016151.4 link	c.-35-118A>G		intron_variant	Intron 1 of 15	ENST00000308893.9	NP_057235.2	Q9UL54-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TAOK2	ENST00000308893.9 link	c.-35-118A>G	intron_variant	Intron 1 of 15	1	NM_016151.4	ENSP00000310094.4	Q9UL54-1
TAOK2	ENST00000543033.5 link	c.-35-118A>G	intron_variant	Intron 1 of 16	1		ENSP00000440336.1	Q9UL54-4
TAOK2	ENST00000279394.7 link	c.-35-118A>G	intron_variant	Intron 1 of 18	1		ENSP00000279394.3	Q9UL54-2

Frequencies

GnomAD3 genomes

AF:

0.360

AC:

54582

AN:

151790

Hom.:

10836

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.344

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.405

Gnomad MID

AF:

0.386

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.353

GnomAD4 exome

AF:

0.440

AC:

357590

AN:

812528

Hom.:

80633

AF XY:

0.442

AC XY:

179785

AN XY:

406972

show subpopulations

African (AFR)

AF:

0.171

AC:

3272

AN:

19100

American (AMR)

AF:

0.331

AC:

6316

AN:

19058

Ashkenazi Jewish (ASJ)

AF:

0.449

AC:

6997

AN:

15592

East Asian (EAS)

AF:

0.357

AC:

11627

AN:

32586

South Asian (SAS)

AF:

0.499

AC:

25375

AN:

50818

European-Finnish (FIN)

AF:

0.398

AC:

12402

AN:

31128

Middle Eastern (MID)

AF:

0.366

AC:

973

AN:

2660

European-Non Finnish (NFE)

AF:

0.455

AC:

274601

AN:

603870

Other (OTH)

AF:

0.425

AC:

16027

AN:

37716

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

9522

19044

28566

38088

47610

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6886

13772

20658

27544

34430

<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:

0.359

AC:

54569

AN:

151908

Hom.:

10834

Cov.:

AF XY:

0.360

AC XY:

26698

AN XY:

74236

show subpopulations

African (AFR)

AF:

0.179

AC:

7427

AN:

41458

American (AMR)

AF:

0.343

AC:

5245

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1523

AN:

3470

East Asian (EAS)

AF:

0.399

AC:

2053

AN:

5148

South Asian (SAS)

AF:

0.489

AC:

2353

AN:

4812

European-Finnish (FIN)

AF:

0.405

AC:

4266

AN:

10542

Middle Eastern (MID)

AF:

0.384

AC:

113

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30420

AN:

67898

Other (OTH)

AF:

0.351

AC:

740

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1739

3478

5218

6957

8696

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

550

1100

1650

2200

2750

<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:

0.418

Hom.:

10922

Bravo

AF:

0.340

Asia WGS

AF:

0.351

AC:

1226

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over