Variant chr13-98446064-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001032296.4(STK24):c.*7109G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.802 in 1,464,782 control chromosomes in the GnomAD database, including 477,714 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 0.76 ( 44488 hom., cov: 35)

Exomes 𝑓: 0.81 ( 433226 hom. )

Consequence

STK24
NM_001032296.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.175

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:

FARP1 (HGNC:3591): (FERM, ARH/RhoGEF and pleckstrin domain protein 1) This gene encodes a protein containing a FERM (4.2, exrin, radixin, moesin) domain, a Dbl homology domain, and two pleckstrin homology domains. These domains are found in guanine nucleotide exchange factors and proteins that link the cytoskeleton to the cell membrane. The encoded protein functions in neurons to promote dendritic growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2013]

FARP1 links:

FARP1 (HGNC:):

FARP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4 linkuse as main transcript	c.*7109G>A		3_prime_UTR_variant	11/11	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
FARP1	NM_005766.4 linkuse as main transcript	c.2797-34C>T		intron_variant		ENST00000319562.11	NP_005757.1	Q9Y4F1-1A0A2X0TVY0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966 linkuse as main transcript	c.*7109G>A		3_prime_UTR_variant	11/11	1	NM_001032296.4	ENSP00000442539.2		Q9Y6E0-2
FARP1	ENST00000319562.11 linkuse as main transcript	c.2797-34C>T		intron_variant		1	NM_005766.4	ENSP00000322926.6		Q9Y4F1-1

Frequencies

GnomAD3 genomes

AF:

0.757

AC:

115197

AN:

152108

Hom.:

44463

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.929

Gnomad AMR

AF:

0.673

Gnomad ASJ

AF:

0.777

Gnomad EAS

AF:

0.628

Gnomad SAS

AF:

0.588

Gnomad FIN

AF:

0.859

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.841

Gnomad OTH

AF:

0.752

GnomAD3 exomes

AF:

0.745

AC:

183227

AN:

246026

Hom.:

70061

AF XY:

0.747

AC XY:

99329

AN XY:

132970

show subpopulations

Gnomad AFR exome

AF:

0.651

Gnomad AMR exome

AF:

0.582

Gnomad ASJ exome

AF:

0.784

Gnomad EAS exome

AF:

0.619

Gnomad SAS exome

AF:

0.600

Gnomad FIN exome

AF:

0.859

Gnomad NFE exome

AF:

0.841

Gnomad OTH exome

AF:

0.768

GnomAD4 exome

AF:

0.808

AC:

1060212

AN:

1312556

Hom.:

433226

Cov.:

AF XY:

0.802

AC XY:

529833

AN XY:

660548

show subpopulations

Gnomad4 AFR exome

AF:

0.646

Gnomad4 AMR exome

AF:

0.590

Gnomad4 ASJ exome

AF:

0.781

Gnomad4 EAS exome

AF:

0.669

Gnomad4 SAS exome

AF:

0.605

Gnomad4 FIN exome

AF:

0.855

Gnomad4 NFE exome

AF:

0.845

Gnomad4 OTH exome

AF:

0.790

GnomAD4 genome

AF:

0.757

AC:

115268

AN:

152226

Hom.:

44488

Cov.:

AF XY:

0.753

AC XY:

56046

AN XY:

74416

show subpopulations

Gnomad4 AFR

AF:

0.656

Gnomad4 AMR

AF:

0.673

Gnomad4 ASJ

AF:

0.777

Gnomad4 EAS

AF:

0.627

Gnomad4 SAS

AF:

0.588

Gnomad4 FIN

AF:

0.859

Gnomad4 NFE

AF:

0.841

Gnomad4 OTH

AF:

0.750

Alfa

AF:

0.797

Hom.:

9097

Bravo

AF:

0.737

Asia WGS

AF:

0.630

AC:

2192

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.4

DANN

Benign

0.39

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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