rs9517320

Positions:

• chr13-98474049-A-C

Variant summary

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

The NM_001032296.4(STK24):​c.597+772T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 152,076 control chromosomes in the GnomAD database, including 22,741 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 0.54 (22741 hom., cov: 32)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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 (NFE) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4	c.597+772T>G		intron_variant		ENST00000539966.6	NP_001027467.2
STK24	NM_001286649.2	c.540+772T>G		intron_variant			NP_001273578.1
STK24	NM_003576.5	c.633+772T>G		intron_variant			NP_003567.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.597+772T>G		intron_variant		1	NM_001032296.4	ENSP00000442539	P1
STK24	ENST00000376547.7	c.633+772T>G		intron_variant		1		ENSP00000365730
STK24	ENST00000444574.1	c.349+772T>G		intron_variant		1		ENSP00000402764
STK24	ENST00000397517.6	c.540+772T>G		intron_variant		2		ENSP00000380651

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82602 AN: 151956 Hom.: 22720 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.544 AC: 82675 AN: 152076 Hom.: 22741 Cov.: 32 AF XY: 0.535 AC XY: 39792 AN XY: 74336

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.495

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.529

Alfa AF: 0.559 Hom.: 18688

Bravo AF: 0.540

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.038
DANN	Benign	0.44

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: rs9517320; hg19: chr13-99126303;