Variant 10-68885540-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_152709.5(STOX1):c.1744C>T(p.Leu582Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,614,176 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0076 ( 8 hom., cov: 32)

Exomes 𝑓: 0.010 ( 103 hom. )

Consequence

STOX1
NM_152709.5 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.315

Variant links:

Genes affected

STOX1 (HGNC:23508): (storkhead box 1) Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in several processes, including positive regulation of G2/M transition of mitotic cell cycle; positive regulation of protein phosphorylation; and regulation of gene expression. Located in centrosome; cytosol; and nuclear lumen. Implicated in pre-eclampsia. Biomarker of Alzheimer's disease. [provided by Alliance of Genome Resources, Apr 2022]

STOX1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005161643).

BP6

Variant 10-68885540-C-T is Benign according to our data. Variant chr10-68885540-C-T is described in ClinVar as [Benign]. Clinvar id is 2640537.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STOX1	NM_152709.5 linkuse as main transcript	c.1744C>T	p.Leu582Phe	missense_variant	3/4	ENST00000298596.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STOX1	ENST00000298596.11 linkuse as main transcript	c.1744C>T	p.Leu582Phe	missense_variant	3/4	1	NM_152709.5	P4	Q6ZVD7-1

Frequencies

GnomAD3 genomes

AF:

0.00756

AC:

1150

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00210

Gnomad AMI

AF:

0.0516

Gnomad AMR

AF:

0.0104

Gnomad ASJ

AF:

0.0231

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00349

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00621

GnomAD3 exomes

AF:

0.00766

AC:

1910

AN:

249376

Hom.:

AF XY:

0.00753

AC XY:

1019

AN XY:

135294

show subpopulations

Gnomad AFR exome

AF:

0.00213

Gnomad AMR exome

AF:

0.00574

Gnomad ASJ exome

AF:

0.0256

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00278

Gnomad FIN exome

AF:

0.00417

Gnomad NFE exome

AF:

0.0103

Gnomad OTH exome

AF:

0.0127

GnomAD4 exome

AF:

0.0105

AC:

15317

AN:

1461884

Hom.:

103

Cov.:

AF XY:

0.0102

AC XY:

7439

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00137

Gnomad4 AMR exome

AF:

0.00635

Gnomad4 ASJ exome

AF:

0.0253

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00293

Gnomad4 FIN exome

AF:

0.00519

Gnomad4 NFE exome

AF:

0.0118

Gnomad4 OTH exome

AF:

0.00985

GnomAD4 genome

AF:

0.00755

AC:

1150

AN:

152292

Hom.:

Cov.:

AF XY:

0.00708

AC XY:

527

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00209

Gnomad4 AMR

AF:

0.0104

Gnomad4 ASJ

AF:

0.0231

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00349

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00614

Alfa

AF:

0.0101

Hom.:

Bravo

AF:

0.00816

TwinsUK

AF:

0.0140

AC:

ALSPAC

AF:

0.0114

AC:

ESP6500AA

AF:

0.00262

AC:

ESP6500EA

AF:

0.0124

AC:

102

ExAC

AF:

0.00794

AC:

960

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

STOX1: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.031

T;T;.

Eigen

Benign

0.010

Eigen_PC

Benign

-0.12

FATHMM_MKL

Benign

0.099

MetaRNN

Benign

0.0052

T;T;T

MetaSVM

Benign

-0.47

MutationAssessor

Uncertain

2.0

M;M;.

MutationTaster

Benign

1.0

N;N;N;N;N

PrimateAI

Benign

0.22

PROVEAN

Benign

-1.5

N;N;.

REVEL

Uncertain

0.31

Sift

Benign

0.093

T;T;.

Sift4G

Uncertain

0.034

D;D;.

Polyphen

1.0

D;D;.

Vest4

0.22

MVP

0.42

MPC

0.33

ClinPred

0.016

GERP RS

5.8

Varity_R

0.11

gMVP

0.018

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over