13-98457465-CT-C

Position:

• chr13-98457465-CT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001032296.4(STK24):​c.1123-162delA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (6497 hom., cov: 0)
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4	c.1123-162delA		intron_variant		ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.1159-162delA		intron_variant			NP_003567.2
STK24	NM_001286649.2	c.1066-162delA		intron_variant			NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.1123-162delA		intron_variant		1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.381 AC: 42156 AN: 110732 Hom.: 6504 Cov.: 0

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.308

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.380 AC: 42132 AN: 110734 Hom.: 6497 Cov.: 0 AF XY: 0.376 AC XY: 19389 AN XY: 51606

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.415

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11351684; hg19: chr13-99109719;