12-118181610-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_016281.4(TAOK3):​c.1330-3C>T variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00275 in 1,613,398 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 8 hom. )

Consequence

TAOK3
NM_016281.4 splice_region, splice_polypyrimidine_tract, intron

Scores

2
Splicing: ADA: 0.04630
2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.81
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 -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 12-118181610-G-A is Benign according to our data. Variant chr12-118181610-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 784674.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 366 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
TAOK3NM_016281.4 linkuse as main transcriptc.1330-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant ENST00000392533.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TAOK3ENST00000392533.8 linkuse as main transcriptc.1330-3C>T splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant 1 NM_016281.4 P1

Frequencies

GnomAD3 genomes
AF:
0.00240
AC:
366
AN:
152188
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000555
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00680
Gnomad ASJ
AF:
0.00115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00325
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.00232
AC:
582
AN:
251074
Hom.:
0
AF XY:
0.00226
AC XY:
306
AN XY:
135692
show subpopulations
Gnomad AFR exome
AF:
0.000431
Gnomad AMR exome
AF:
0.00668
Gnomad ASJ exome
AF:
0.000397
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000186
Gnomad NFE exome
AF:
0.00269
Gnomad OTH exome
AF:
0.00506
GnomAD4 exome
AF:
0.00279
AC:
4070
AN:
1461092
Hom.:
8
Cov.:
31
AF XY:
0.00268
AC XY:
1946
AN XY:
726824
show subpopulations
Gnomad4 AFR exome
AF:
0.000538
Gnomad4 AMR exome
AF:
0.00718
Gnomad4 ASJ exome
AF:
0.000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.000338
Gnomad4 NFE exome
AF:
0.00320
Gnomad4 OTH exome
AF:
0.00227
GnomAD4 genome
AF:
0.00240
AC:
366
AN:
152306
Hom.:
2
Cov.:
32
AF XY:
0.00244
AC XY:
182
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.000553
Gnomad4 AMR
AF:
0.00679
Gnomad4 ASJ
AF:
0.00115
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00325
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00248
Hom.:
1
Bravo
AF:
0.00279
EpiCase
AF:
0.00322
EpiControl
AF:
0.00344

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.44
CADD
Benign
16
DANN
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.046
dbscSNV1_RF
Benign
0.26
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: rs77139493; hg19: chr12-118619415; API