rs514826

Variant names:

• chr12-118371498-A-C
• rs514826
• NM_016281.4:c.-194+1150T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-118371498-A-C
• chr12-118371498-A-G
• chr12-118371498-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016281.4(TAOK3):​c.-194+1150T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: TAOK3 NM_016281.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016281.4. 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.-194+1150T>G		intron	N/A	NP_057365.3
	TAOK3	NM_001346487.2		c.-194+1150T>G		intron	N/A	NP_001333416.1
	TAOK3	NM_001346488.2		c.-371+1150T>G		intron	N/A	NP_001333417.1	Q9H2K8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TAOK3	ENST00000392533.8	TSL:1 MANE Select	c.-194+1150T>G		intron	N/A	ENSP00000376317.3	Q9H2K8
	TAOK3	ENST00000894342.1		c.-336+1150T>G		intron	N/A	ENSP00000564401.1
	TAOK3	ENST00000967759.1		c.-513+1150T>G		intron	N/A	ENSP00000637818.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 56657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.44
PhyloP100		-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs514826; hg19: chr12-118809303;