10-68827801-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.96

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]

ACMG classification

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	UniProt
STOX1	NM_152709.5	c.178C>T	p.Leu60=	synonymous_variant	1/4	ENST00000298596.11
STOX1	NM_001130161.4	c.178C>T	p.Leu60=	synonymous_variant	1/5
STOX1	NM_001130159.3	c.178C>T	p.Leu60=	synonymous_variant	1/4
STOX1	NM_001130160.3	c.178C>T	p.Leu60=	synonymous_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STOX1	ENST00000298596.11	c.178C>T	p.Leu60=	synonymous_variant	1/4	1	NM_152709.5	P4

Frequencies

GnomAD3 genomes AF: 0.000302 AC: 25 AN: 82734 Hom.: 0 Cov.: 10

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.: 1 Cov.: 6 AF XY: 0.000245 AC XY: 51 AN XY: 208546

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: 25 AN: 82808 Hom.: 0 Cov.: 10 AF XY: 0.000393 AC XY: 16 AN XY: 40692

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.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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	15
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

Other links and lift over

dbSNP: rs1253783868; hg19: chr10-70587558;