Variant 16-29977895-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2

The NM_016151.4(TAOK2):c.123C>T(p.Ala41=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0194 in 1,614,112 control chromosomes in the GnomAD database, including 357 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.013 ( 15 hom., cov: 32)

Exomes 𝑓: 0.020 ( 342 hom. )

Consequence

TAOK2
NM_016151.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.15

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 16-29977895-C-T is Benign according to our data. Variant chr16-29977895-C-T is described in ClinVar as [Benign]. Clinvar id is 1168779.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-2.15 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0132 (2004/152260) while in subpopulation NFE AF= 0.0193 (1312/68020). AF 95% confidence interval is 0.0184. There are 15 homozygotes in gnomad4. There are 942 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2004 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAOK2	NM_016151.4 linkuse as main transcript	c.123C>T	p.Ala41=	synonymous_variant	2/16	ENST00000308893.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAOK2	ENST00000308893.9 linkuse as main transcript	c.123C>T	p.Ala41=	synonymous_variant	2/16	1	NM_016151.4		Q9UL54-1
TAOK2	ENST00000543033.5 linkuse as main transcript	c.123C>T	p.Ala41=	synonymous_variant	2/17	1			Q9UL54-4
TAOK2	ENST00000279394.7 linkuse as main transcript	c.123C>T	p.Ala41=	synonymous_variant	2/19	1		P1	Q9UL54-2

Frequencies

GnomAD3 genomes

AF:

0.0132

AC:

2005

AN:

152142

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00338

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0171

Gnomad ASJ

AF:

0.0239

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00787

Gnomad FIN

AF:

0.0136

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0193

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.0149

AC:

3744

AN:

251406

Hom.:

AF XY:

0.0152

AC XY:

2063

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.00265

Gnomad AMR exome

AF:

0.0133

Gnomad ASJ exome

AF:

0.0256

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00918

Gnomad FIN exome

AF:

0.0148

Gnomad NFE exome

AF:

0.0197

Gnomad OTH exome

AF:

0.0223

GnomAD4 exome

AF:

0.0201

AC:

29364

AN:

1461852

Hom.:

342

Cov.:

AF XY:

0.0198

AC XY:

14405

AN XY:

727242

show subpopulations

Gnomad4 AFR exome

AF:

0.00275

Gnomad4 AMR exome

AF:

0.0135

Gnomad4 ASJ exome

AF:

0.0257

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00997

Gnomad4 FIN exome

AF:

0.0146

Gnomad4 NFE exome

AF:

0.0227

Gnomad4 OTH exome

AF:

0.0173

GnomAD4 genome

AF:

0.0132

AC:

2004

AN:

152260

Hom.:

Cov.:

AF XY:

0.0127

AC XY:

942

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.00337

Gnomad4 AMR

AF:

0.0170

Gnomad4 ASJ

AF:

0.0239

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00788

Gnomad4 FIN

AF:

0.0136

Gnomad4 NFE

AF:

0.0193

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0173

Hom.:

Bravo

AF:

0.0123

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.0161

EpiControl

AF:

0.0170

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

5.0

DANN

Benign

0.74

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over