13-98457465-CTTTTTTTTTTT-CTTTTTTTTTTTTT

Variant names:

• chr13-98457465-C-CTT
• rs11351684
• NM_001032296.4:c.1123-163_1123-162dupAA

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001032296.4(STK24):​c.1123-163_1123-162dupAA 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 0.0084 (12 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 12 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.1123-163_1123-162dupAA		intron_variant	Intron 9 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.1159-163_1159-162dupAA		intron_variant	Intron 9 of 10		NP_003567.2
STK24	NM_001286649.2	c.1066-163_1066-162dupAA		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.1123-162_1123-161insAA		intron_variant	Intron 9 of 10	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.00841 AC: 932 AN: 110782 Hom.: 12 Cov.: 0

Gnomad AFR AF: 0.00518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00730

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.000507

Gnomad SAS AF: 0.00516

Gnomad FIN AF: 0.00385

Gnomad MID AF: 0.0167

Gnomad NFE AF: 0.0104

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.00843 AC: 934 AN: 110784 Hom.: 12 Cov.: 0 AF XY: 0.00806 AC XY: 416 AN XY: 51616

African (AFR) AF: 0.00517 AC: 152 AN: 29378

American (AMR) AF: 0.00729 AC: 78 AN: 10694

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 82 AN: 2924

East Asian (EAS) AF: 0.000508 AC: 2 AN: 3936

South Asian (SAS) AF: 0.00519 AC: 18 AN: 3466

European-Finnish (FIN) AF: 0.00385 AC: 15 AN: 3898

Middle Eastern (MID) AF: 0.0180 AC: 4 AN: 222

European-Non Finnish (NFE) AF: 0.0104 AC: 563 AN: 54128

Other (OTH) AF: 0.0136 AC: 20 AN: 1466

Alfa AF: 0.00485 Hom.: 189

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11351684; hg19: chr13-99109719;