13-98497756-C-T

Variant names:

• chr13-98497756-C-T
• rs7338502
• NM_001032296.4:c.274-15435G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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 -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 rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.274-15435G>A		intron_variant	Intron 2 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.310-15435G>A		intron_variant	Intron 2 of 10		NP_003567.2
STK24	NM_001286649.2	c.273+21487G>A		intron_variant	Intron 2 of 9		NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.274-15435G>A		intron_variant	Intron 2 of 10	1	NM_001032296.4	ENSP00000442539.2

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

African (AFR) AF: 0.104 AC: 4308 AN: 41554

American (AMR) AF: 0.0490 AC: 750 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3472

East Asian (EAS) AF: 0.0649 AC: 336 AN: 5174

South Asian (SAS) AF: 0.120 AC: 578 AN: 4816

European-Finnish (FIN) AF: 0.0243 AC: 258 AN: 10612

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0465 AC: 3165 AN: 68032

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0620 Hom.: 56

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
PhyloP100		0.0040
Mutation Taster		=100/0	polymorphism (auto)

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: rs7338502; hg19: chr13-99150010;