NM_001032296.4:c.1123-164_1123-162delAAA

Variant names:

• chr13-98457465-CTTT-C
• rs11351684
• NM_001032296.4:c.1123-164_1123-162delAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001032296.4(STK24):​c.1123-164_1123-162delAAA 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 0.0036 (1 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 1 publications found

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

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.1123-164_1123-162delAAA		intron_variant	Intron 9 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.1159-164_1159-162delAAA		intron_variant	Intron 9 of 10		NP_003567.2
STK24	NM_001286649.2	c.1066-164_1066-162delAAA		intron_variant	Intron 8 of 9		NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.1123-164_1123-162delAAA		intron_variant	Intron 9 of 10	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.00361 AC: 400 AN: 110780 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00197

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000507

Gnomad SAS AF: 0.000287

Gnomad FIN AF: 0.00565

Gnomad MID AF: 0.0125

Gnomad NFE AF: 0.000702

Gnomad OTH AF: 0.00550

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

GnomAD4 genome AF: 0.00364 AC: 403 AN: 110780 Hom.: 1 Cov.: 0 AF XY: 0.00409 AC XY: 211 AN XY: 51624

African (AFR) AF: 0.0104 AC: 307 AN: 29380

American (AMR) AF: 0.00196 AC: 21 AN: 10696

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2928

East Asian (EAS) AF: 0.000763 AC: 3 AN: 3932

South Asian (SAS) AF: 0.000289 AC: 1 AN: 3466

European-Finnish (FIN) AF: 0.00565 AC: 22 AN: 3892

Middle Eastern (MID) AF: 0.0135 AC: 3 AN: 222

European-Non Finnish (NFE) AF: 0.000702 AC: 38 AN: 54126

Other (OTH) AF: 0.00546 AC: 8 AN: 1466

Alfa AF: 0.00 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.010
Mutation Taster		=100/0	polymorphism

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: rs11351684; hg19: chr13-99109719;