13-98479040-C-T

Variant names:

• chr13-98479040-C-T
• rs912330
• NM_001032296.4:c.330+3225G>A

Variant summary

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

The NM_001032296.4(STK24):​c.330+3225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,144 control chromosomes in the GnomAD database, including 6,125 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 0.27 (6125 hom., cov: 32)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4	c.330+3225G>A		intron_variant	Intron 3 of 10	ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.366+3225G>A		intron_variant	Intron 3 of 10		NP_003567.2
STK24	NM_001286649.2	c.274-3682G>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.330+3225G>A		intron_variant	Intron 3 of 10	1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40777 AN: 152026 Hom.: 6127 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.268 AC: 40765 AN: 152144 Hom.: 6125 Cov.: 32 AF XY: 0.272 AC XY: 20252 AN XY: 74368

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.269

Alfa AF: 0.300 Hom.: 7163

Bravo AF: 0.256

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.73
DANN	Benign	0.74

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: rs912330; hg19: chr13-99131294;