Variant chr10-68827801-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_152709.5(STOX1):c.178C>T(p.Leu60=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00030 ( 0 hom., cov: 10)

Exomes 𝑓: 0.00027 ( 1 hom. )

Failed GnomAD Quality Control

Consequence

STOX1
NM_152709.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.96

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 -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.5).

BP6

Variant 10-68827801-C-T is Benign according to our data. Variant chr10-68827801-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2640535.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.96 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
STOX1	NM_152709.5 linkuse as main transcript	c.178C>T	p.Leu60=	synonymous_variant	1/4	ENST00000298596.11	NP_689922.3
STOX1	NM_001130161.4 linkuse as main transcript	c.178C>T	p.Leu60=	synonymous_variant	1/5		NP_001123633.1
STOX1	NM_001130159.3 linkuse as main transcript	c.178C>T	p.Leu60=	synonymous_variant	1/4		NP_001123631.1
STOX1	NM_001130160.3 linkuse as main transcript	c.178C>T	p.Leu60=	synonymous_variant	1/3		NP_001123632.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STOX1	ENST00000298596.11 linkuse as main transcript	c.178C>T	p.Leu60=	synonymous_variant	1/4	1	NM_152709.5	ENSP00000298596	P4	Q6ZVD7-1

Frequencies

GnomAD3 genomes

AF:

0.000302

AC:

AN:

82734

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000504

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00153

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000315

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000270

AC:

119

AN:

441260

Hom.:

Cov.:

AF XY:

0.000245

AC XY:

AN XY:

208546

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000423

Gnomad4 NFE exome

AF:

0.000276

Gnomad4 OTH exome

AF:

0.000536

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000302

AC:

AN:

82808

Hom.:

Cov.:

AF XY:

0.000393

AC XY:

AN XY:

40692

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000503

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00153

Gnomad4 NFE

AF:

0.000315

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000552

Hom.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

STOX1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

DANN

Uncertain

0.99

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