chr13-98482066-C-CA

Variant names:

• chr13-98482066-C-CA
• rs34520150
• NM_001032296.4:c.330+198dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001032296.4(STK24):​c.330+198dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0237 in 99,842 control chromosomes in the GnomAD database, including 35 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.024 (35 hom., cov: 31)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0554 is higher than 0.05.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	NM_001032296.4	MANE Select	c.330+198dupT		intron	N/A	NP_001027467.2	Q9Y6E0-2
	STK24	NM_003576.5		c.366+198dupT		intron	N/A	NP_003567.2
	STK24	NM_001286649.2		c.274-6709dupT		intron	N/A	NP_001273578.1	B4DR80

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STK24	ENST00000539966.6	TSL:1 MANE Select	c.330+198_330+199insT		intron	N/A	ENSP00000442539.2	Q9Y6E0-2
	STK24	ENST00000376547.7	TSL:1	c.366+198_366+199insT		intron	N/A	ENSP00000365730.3	Q9Y6E0-1
	STK24	ENST00000444574.1	TSL:1	c.81+198_81+199insT		intron	N/A	ENSP00000402764.1	H0Y630

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 2348 AN: 99812 Hom.: 32 Cov.: 31

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.00116

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.0102

Gnomad FIN AF: 0.00441

Gnomad MID AF: 0.0247

Gnomad NFE AF: 0.00913

Gnomad OTH AF: 0.0316

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

GnomAD4 genome AF: 0.0237 AC: 2366 AN: 99842 Hom.: 35 Cov.: 31 AF XY: 0.0249 AC XY: 1164 AN XY: 46732

African (AFR) AF: 0.0578 AC: 1574 AN: 27222

American (AMR) AF: 0.0167 AC: 158 AN: 9478

Ashkenazi Jewish (ASJ) AF: 0.00116 AC: 3 AN: 2584

East Asian (EAS) AF: 0.0297 AC: 101 AN: 3402

South Asian (SAS) AF: 0.00989 AC: 30 AN: 3034

European-Finnish (FIN) AF: 0.00441 AC: 20 AN: 4536

Middle Eastern (MID) AF: 0.0278 AC: 4 AN: 144

European-Non Finnish (NFE) AF: 0.00913 AC: 434 AN: 47522

Other (OTH) AF: 0.0314 AC: 42 AN: 1336

Alfa AF: 0.000769 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9
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: rs34520150; hg19: chr13-99134320;