chr12-118313188-C-T

Variant names:

• chr12-118313188-C-T
• rs7309671
• NM_016281.4:c.-193-46429G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001346487.2(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_001346487.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001346487.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAOK3	NM_016281.4	MANE Select	c.-193-46429G>A		intron	N/A	NP_057365.3
	TAOK3	NM_001346487.2		c.-193-46429G>A		intron	N/A	NP_001333416.1
	TAOK3	NM_001346488.2		c.-370-46429G>A		intron	N/A	NP_001333417.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAOK3	ENST00000392533.8	TSL:1 MANE Select	c.-193-46429G>A		intron	N/A	ENSP00000376317.3
	TAOK3	ENST00000419821.6	TSL:1	c.-194+46318G>A		intron	N/A	ENSP00000416374.2
	TAOK3	ENST00000894342.1		c.-335-17807G>A		intron	N/A	ENSP00000564401.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15563 AN: 152080 Hom.: 995 Cov.: 32

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

African (AFR) AF: 0.0328 AC: 1364 AN: 41556

American (AMR) AF: 0.102 AC: 1552 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3470

East Asian (EAS) AF: 0.0104 AC: 54 AN: 5186

South Asian (SAS) AF: 0.0587 AC: 283 AN: 4820

European-Finnish (FIN) AF: 0.164 AC: 1734 AN: 10554

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9784 AN: 68002

Other (OTH) AF: 0.0931 AC: 197 AN: 2116

Alfa AF: 0.118 Hom.: 199

Bravo AF: 0.0931

Asia WGS AF: 0.0290 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.15
PhyloP100		-0.087
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7309671; hg19: chr12-118750993;