rs7309671

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016281.4(TAOK3):​c.-193-46429G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,198 control chromosomes in the GnomAD database, including 996 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 ( 996 hom., cov: 32)

Consequence

TAOK3
NM_016281.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0870
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TAOK3NM_016281.4 linkuse as main transcriptc.-193-46429G>A intron_variant ENST00000392533.8 NP_057365.3 Q9H2K8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TAOK3ENST00000392533.8 linkuse as main transcriptc.-193-46429G>A intron_variant 1 NM_016281.4 ENSP00000376317.3 Q9H2K8

Frequencies

GnomAD3 genomes
AF:
0.102
AC:
15563
AN:
152080
Hom.:
995
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0329
Gnomad AMI
AF:
0.0625
Gnomad AMR
AF:
0.102
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.0104
Gnomad SAS
AF:
0.0578
Gnomad FIN
AF:
0.164
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.144
Gnomad OTH
AF:
0.0922
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.102
AC:
15559
AN:
152198
Hom.:
996
Cov.:
32
AF XY:
0.101
AC XY:
7528
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.0328
Gnomad4 AMR
AF:
0.102
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.0104
Gnomad4 SAS
AF:
0.0587
Gnomad4 FIN
AF:
0.164
Gnomad4 NFE
AF:
0.144
Gnomad4 OTH
AF:
0.0931
Alfa
AF:
0.121
Hom.:
198
Bravo
AF:
0.0931
Asia WGS
AF:
0.0290
AC:
104
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.41
DANN
Benign
0.15

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs7309671; hg19: chr12-118750993; API