GeneBe

rs11351684

Positions:

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001032296.4(STK24):​c.1123-172_1123-162delAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

STK24
NM_001032296.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89
Variant links:
Genes affected
STK24 (HGNC:11403): (serine/threonine kinase 24) This gene encodes a serine/threonine protein kinase that functions upstream of mitogen-activated protein kinase (MAPK) signaling. The encoded protein is cleaved into two chains by caspases; the N-terminal fragment (MST3/N) translocates to the nucleus and promotes programmed cells death. There is a pseudogene for this gene on chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
STK24NM_001032296.4 linkuse as main transcriptc.1123-172_1123-162delAAAAAAAAAAA intron_variant ENST00000539966.6 NP_001027467.2 Q9Y6E0-2Q5U0E6Q6P0Y1
STK24NM_003576.5 linkuse as main transcriptc.1159-172_1159-162delAAAAAAAAAAA intron_variant NP_003567.2 Q9Y6E0-1
STK24NM_001286649.2 linkuse as main transcriptc.1066-172_1066-162delAAAAAAAAAAA intron_variant NP_001273578.1 B4DR80

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
STK24ENST00000539966.6 linkuse as main transcriptc.1123-172_1123-162delAAAAAAAAAAA intron_variant 1 NM_001032296.4 ENSP00000442539.2 Q9Y6E0-2

Frequencies

GnomAD3 genomes
Cov.:
0
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs11351684; hg19: chr13-99109719; API