rs7338502

chr13-98497756-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001032296.4(STK24):c.274-15435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,274 control chromosomes in the GnomAD database, including 391 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (391 hom., cov: 33)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STK24	NM_001032296.4	c.274-15435G>A		intron_variant		ENST00000539966.6
STK24	NM_001286649.2	c.273+21487G>A		intron_variant
STK24	NM_003576.5	c.310-15435G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6	c.274-15435G>A		intron_variant		1	NM_001032296.4	P1

Frequencies

GnomAD3 genomes AF: 0.0641 AC: 9760 AN: 152156 Hom.: 392 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0243

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0465

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0641 AC: 9766 AN: 152274 Hom.: 391 Cov.: 33 AF XY: 0.0640 AC XY: 4768 AN XY: 74454

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0490

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.0649

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0243

Gnomad4 NFE AF: 0.0465

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.0601 Hom.: 51

Bravo AF: 0.0665

Asia WGS AF: 0.0650 AC: 226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.6
Dann	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs7338502; hg19: chr13-99150010;