13-98457465-C-CTTTTTT

Variant names:

• chr13-98457465-C-CTTTTTT
• rs11351684
• NM_001032296.4:c.1123-167_1123-162dupAAAAAA

Variant summary

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

The NM_001032296.4(STK24):​c.1123-167_1123-162dupAAAAAA 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 0.000027 (0 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: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001032296.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.1123-167_1123-162dupAAAAAA		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.1159-167_1159-162dupAAAAAA		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.1066-167_1066-162dupAAAAAA		intron	N/A	NP_001273578.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.1123-162_1123-161insAAAAAA		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.1159-162_1159-161insAAAAAA		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.874-162_874-161insAAAAAA		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.0000271 AC: 3 AN: 110812 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000341

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000287

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000185

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000271 AC: 3 AN: 110812 Hom.: 0 Cov.: 0 AF XY: 0.0000388 AC XY: 2 AN XY: 51610

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000341 AC: 1 AN: 29340

American (AMR) AF: 0.00 AC: 0 AN: 10684

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 3948

South Asian (SAS) AF: 0.000287 AC: 1 AN: 3490

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3898

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.0000185 AC: 1 AN: 54158

Other (OTH) AF: 0.00 AC: 0 AN: 1454

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.0000416442), which strongly suggests a high chance of mosaicism in these individuals.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.93

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;