Variant 13-98446216-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.*6957G>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 0.773 in 1,593,296 control chromosomes in the GnomAD database, including 487,323 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 0.68 ( 37452 hom., cov: 33)

Exomes 𝑓: 0.78 ( 449871 hom. )

Consequence

STK24
NM_001032296.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0520

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:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 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.*6957G>A		3_prime_UTR_variant	11/11	ENST00000539966.6	NP_001027467.2
FARP1	NM_005766.4 linkuse as main transcript	c.2904+11C>T		intron_variant		ENST00000319562.11	NP_005757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STK24	ENST00000539966.6 linkuse as main transcript	c.*6957G>A		3_prime_UTR_variant	11/11	1	NM_001032296.4	ENSP00000442539	P1	Q9Y6E0-2
FARP1	ENST00000319562.11 linkuse as main transcript	c.2904+11C>T		intron_variant		1	NM_005766.4	ENSP00000322926	P1	Q9Y4F1-1

Frequencies

GnomAD3 genomes

AF:

0.679

AC:

103293

AN:

152056

Hom.:

37447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.433

Gnomad AMI

AF:

0.927

Gnomad AMR

AF:

0.640

Gnomad ASJ

AF:

0.737

Gnomad EAS

AF:

0.613

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.838

Gnomad MID

AF:

0.620

Gnomad NFE

AF:

0.821

Gnomad OTH

AF:

0.681

GnomAD3 exomes

AF:

0.709

AC:

176894

AN:

249438

Hom.:

65336

AF XY:

0.714

AC XY:

96320

AN XY:

134838

show subpopulations

Gnomad AFR exome

AF:

0.426

Gnomad AMR exome

AF:

0.565

Gnomad ASJ exome

AF:

0.740

Gnomad EAS exome

AF:

0.602

Gnomad SAS exome

AF:

0.564

Gnomad FIN exome

AF:

0.838

Gnomad NFE exome

AF:

0.821

Gnomad OTH exome

AF:

0.738

GnomAD4 exome

AF:

0.783

AC:

1128905

AN:

1441122

Hom.:

449871

Cov.:

AF XY:

0.778

AC XY:

558573

AN XY:

718032

show subpopulations

Gnomad4 AFR exome

AF:

0.417

Gnomad4 AMR exome

AF:

0.570

Gnomad4 ASJ exome

AF:

0.742

Gnomad4 EAS exome

AF:

0.638

Gnomad4 SAS exome

AF:

0.567

Gnomad4 FIN exome

AF:

0.835

Gnomad4 NFE exome

AF:

0.826

Gnomad4 OTH exome

AF:

0.753

GnomAD4 genome

AF:

0.679

AC:

103319

AN:

152174

Hom.:

37452

Cov.:

AF XY:

0.676

AC XY:

50289

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.433

Gnomad4 AMR

AF:

0.640

Gnomad4 ASJ

AF:

0.737

Gnomad4 EAS

AF:

0.613

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.838

Gnomad4 NFE

AF:

0.821

Gnomad4 OTH

AF:

0.678

Alfa

AF:

0.730

Hom.:

13449

Bravo

AF:

0.653

Asia WGS

AF:

0.593

AC:

2062

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.41

DANN

Benign

0.40

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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