13-98463584-TAAAAA-TAAAA

Position:

• chr13-98463584-TAAAAA-TAAAA

Variant summary

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

The NM_001032296.4(STK24):​c.929+106delT 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 0.92 (61163 hom., cov: 0)
  • Exomes 𝑓: 0.51 (10878 hom.)
  • Failed GnomAD Quality Control
• Consequence: STK24 NM_001032296.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

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 = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4	c.929+106delT		intron_variant		ENST00000539966.6	NP_001027467.2
STK24	NM_003576.5	c.965+106delT		intron_variant			NP_003567.2
STK24	NM_001286649.2	c.872+106delT		intron_variant			NP_001273578.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6	c.929+106delT		intron_variant		1	NM_001032296.4	ENSP00000442539.2

Frequencies

GnomAD3 genomes AF: 0.924 AC: 131569 AN: 142458 Hom.: 61167 Cov.: 0

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.975

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.935

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.507 AC: 459705 AN: 906260 Hom.: 10878 AF XY: 0.507 AC XY: 226575 AN XY: 447022

Gnomad4 AFR exome AF: 0.460

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.503

Gnomad4 EAS exome AF: 0.502

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.508

Gnomad4 NFE exome AF: 0.509

Gnomad4 OTH exome AF: 0.505

GnomAD4 genome AF: 0.923 AC: 131577 AN: 142490 Hom.: 61163 Cov.: 0 AF XY: 0.923 AC XY: 63625 AN XY: 68948

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.975

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.986

Gnomad4 OTH AF: 0.934

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: rs56325686; hg19: chr13-99115838;