Variant 13-98463584-TAAAAA-TAAAA details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001032296.4(STK24):c.929+106del 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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

Variant links:

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]

STK24 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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	Effect	MANE
STK24	NM_001032296.4 linkuse as main transcript	c.929+106del	intron_variant	ENST00000539966.6
STK24	NM_001286649.2 linkuse as main transcript	c.872+106del	intron_variant
STK24	NM_003576.5 linkuse as main transcript	c.965+106del	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STK24	ENST00000539966.6 linkuse as main transcript	c.929+106del		intron_variant		1	NM_001032296.4	P1	Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.924

AC:

131569

AN:

142458

Hom.:

61167

Cov.:

show subpopulations

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

show subpopulations

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.:

AF XY:

0.923

AC XY:

63625

AN XY:

68948

show subpopulations

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

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over