13-98457465-CTTTTTTTTTTT-CTTTTTTT

Position:

• chr13-98457465-CTTTTTTTTTTT-CTTTTTTT

Variant summary

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

The NM_001032296.4(STK24):​c.1123-165_1123-162delAAAA 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: 𝑓 0.00035 (0 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4	c.1123-165_1123-162delAAAA		intron_variant		ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.1159-165_1159-162delAAAA		intron_variant			NP_003567.2
STK24	NM_001286649.2	c.1066-165_1066-162delAAAA		intron_variant			NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.1123-165_1123-162delAAAA		intron_variant		1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.000352 AC: 39 AN: 110790 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000852

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000187

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000253

Gnomad SAS AF: 0.000573

Gnomad FIN AF: 0.000770

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000111

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000352 AC: 39 AN: 110792 Hom.: 0 Cov.: 0 AF XY: 0.000504 AC XY: 26 AN XY: 51622

Gnomad4 AFR AF: 0.000851

Gnomad4 AMR AF: 0.000187

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000254

Gnomad4 SAS AF: 0.000577

Gnomad4 FIN AF: 0.000770

Gnomad4 NFE AF: 0.000111

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11351684; hg19: chr13-99109719;