Variant rs9517310 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.*4953G>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 0.278 in 1,607,738 control chromosomes in the GnomAD database, including 64,944 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 0.23 ( 4629 hom., cov: 33)

Exomes 𝑓: 0.28 ( 60315 hom. )

Consequence

STK24
NM_001032296.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.211

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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STK24	NM_001032296.4 link	c.*4953G>A		3_prime_UTR_variant	11/11	ENST00000539966.6	NP_001027467.2	Q9Y6E0-2Q5U0E6Q6P0Y1
FARP1	NM_005766.4 link	c.3057-16C>T		intron_variant		ENST00000319562.11	NP_005757.1	Q9Y4F1-1A0A2X0TVY0

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
STK24	ENST00000539966 link	c.*4953G>A	3_prime_UTR_variant	11/11	1	NM_001032296.4	ENSP00000442539.2	Q9Y6E0-2
FARP1	ENST00000319562.11 link	c.3057-16C>T	intron_variant		1	NM_005766.4	ENSP00000322926.6	Q9Y4F1-1
FARP1	ENST00000595437.5 link	c.3150-16C>T	intron_variant		1		ENSP00000471242.1	C9JME2
FARP1	ENST00000627049.2 link	c.3150-16C>T	intron_variant		5		ENSP00000486285.1	C9JME2

Frequencies

GnomAD3 genomes

AF:

0.234

AC:

35572

AN:

152054

Hom.:

4626

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.318

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.258

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.239

GnomAD3 exomes

AF:

0.250

AC:

62752

AN:

251134

Hom.:

8378

AF XY:

0.254

AC XY:

34433

AN XY:

135718

show subpopulations

Gnomad AFR exome

AF:

0.123

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.263

Gnomad EAS exome

AF:

0.159

Gnomad SAS exome

AF:

0.227

Gnomad FIN exome

AF:

0.247

Gnomad NFE exome

AF:

0.299

Gnomad OTH exome

AF:

0.248

GnomAD4 exome

AF:

0.283

AC:

411764

AN:

1455566

Hom.:

60315

Cov.:

AF XY:

0.282

AC XY:

204544

AN XY:

724462

show subpopulations

Gnomad4 AFR exome

AF:

0.116

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.262

Gnomad4 EAS exome

AF:

0.144

Gnomad4 SAS exome

AF:

0.230

Gnomad4 FIN exome

AF:

0.258

Gnomad4 NFE exome

AF:

0.303

Gnomad4 OTH exome

AF:

0.264

GnomAD4 genome

AF:

0.234

AC:

35583

AN:

152172

Hom.:

4629

Cov.:

AF XY:

0.230

AC XY:

17108

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.258

Gnomad4 EAS

AF:

0.154

Gnomad4 SAS

AF:

0.211

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.306

Gnomad4 OTH

AF:

0.238

Alfa

AF:

0.284

Hom.:

8839

Bravo

AF:

0.226

Asia WGS

AF:

0.184

AC:

640

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

1.9

DANN

Benign

0.72

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