chr13-98460215-G-GCCTGACA

Variant names:

• chr13-98460215-G-GCCTGACA
• rs35458785
• NM_001032296.4:c.1122+156_1122+157insTGTCAGG

Variant summary

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

The NM_001032296.4(STK24):​c.1122+156_1122+157insTGTCAGG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 9,548 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0034 (0 hom., cov: 33)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558
• Publications: 0 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.1122+156_1122+157insTGTCAGG		intron	N/A	NP_001027467.2
	STK24	NM_003576.5		c.1158+156_1158+157insTGTCAGG		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.1065+156_1065+157insTGTCAGG		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.1122+156_1122+157insTGTCAGG		intron	N/A	ENSP00000442539.2
	STK24	ENST00000376547.7	TSL:1	c.1158+156_1158+157insTGTCAGG		intron	N/A	ENSP00000365730.3
	STK24	ENST00000444574.1	TSL:1	c.873+156_873+157insTGTCAGG		intron	N/A	ENSP00000402764.1

Frequencies

GnomAD3 genomes AF: 0.00336 AC: 32 AN: 9522 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00281

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0208

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

GnomAD4 genome AF: 0.00335 AC: 32 AN: 9548 Hom.: 0 Cov.: 33 AF XY: 0.00399 AC XY: 19 AN XY: 4762

African (AFR) AF: 0.00 AC: 0 AN: 6018

American (AMR) AF: 0.00 AC: 0 AN: 1524

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 104

East Asian (EAS) AF: 0.00279 AC: 1 AN: 358

South Asian (SAS) AF: 0.00 AC: 0 AN: 540

European-Finnish (FIN) AF: 0.0743 AC: 15 AN: 202

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 12

European-Non Finnish (NFE) AF: 0.0202 AC: 14 AN: 694

Other (OTH) AF: 0.0208 AC: 2 AN: 96

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000604

Asia WGS AF: 0.00541 AC: 8 AN: 1480

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.56
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: rs35458785; hg19: chr13-99112469;