rs7314987

chr12-118274072-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016281.4(TAOK3):c.-193-7313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 151,876 control chromosomes in the GnomAD database, including 852 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 0.094 (852 hom., cov: 32)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TAOK3	NM_016281.4	c.-193-7313G>A		intron_variant		ENST00000392533.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAOK3	ENST00000392533.8	c.-193-7313G>A		intron_variant		1	NM_016281.4	P1

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14269 AN: 151758 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.0306

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00984

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0774

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0939 AC: 14265 AN: 151876 Hom.: 852 Cov.: 32 AF XY: 0.0934 AC XY: 6929 AN XY: 74194

Gnomad4 AFR AF: 0.0305

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00986

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.0785

Alfa AF: 0.112 Hom.: 175

Bravo AF: 0.0838

Asia WGS AF: 0.0250 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.50

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

Other links and lift over

dbSNP: rs7314987; hg19: chr12-118711877;