Genetic Variant NM_001032296.4:c.929+105_929+106dupTT (chr13-98463584-T-TAA) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001032296.4(STK24):c.929+105_929+106dupTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000714 in 1,047,230 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000014 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00082 ( 0 hom. )

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 Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
STK24	NM_001032296.4 link	c.929+105_929+106dupTT	intron_variant	Intron 7 of 10	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
STK24	NM_003576.5 link	c.965+105_965+106dupTT	intron_variant	Intron 7 of 10		NP_003567.2	Q9Y6E0-1
STK24	NM_001286649.2 link	c.872+105_872+106dupTT	intron_variant	Intron 6 of 9		NP_001273578.1	B4DR80

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6 link	c.929+106_929+107insTT		intron_variant	Intron 7 of 10	1	NM_001032296.4	ENSP00000442539.2		Q9Y6E0-2

Frequencies

GnomAD3 genomes

AF:

0.0000140

AC:

AN:

142408

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000447

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000825

AC:

746

AN:

904790

Hom.:

AF XY:

0.000925

AC XY:

413

AN XY:

446298

show subpopulations

Gnomad4 AFR exome

AF:

0.00311

Gnomad4 AMR exome

AF:

0.00122

Gnomad4 ASJ exome

AF:

0.00115

Gnomad4 EAS exome

AF:

0.000353

Gnomad4 SAS exome

AF:

0.00345

Gnomad4 FIN exome

AF:

0.000390

Gnomad4 NFE exome

AF:

0.000576

Gnomad4 OTH exome

AF:

0.00112

GnomAD4 genome

AF:

0.0000140

AC:

AN:

142440

Hom.:

Cov.:

AF XY:

0.0000145

AC XY:

AN XY:

68926

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000449

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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