NM_152709.5:c.134C>G

Variant names:

• chr10-68827757-C-G
• rs1386133319
• NM_152709.5:c.134C>G

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_152709.5(STOX1):​c.134C>G​(p.Ala45Gly) variant causes a missense 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 Uncertain significance (★).

• Frequency: Genomes: 𝑓 0.000018 (0 hom., cov: 13)
• Consequence: STOX1 NM_152709.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.800
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.42173555).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152709.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOX1	NM_152709.5	MANE Select	c.134C>G	p.Ala45Gly	missense	Exon 1 of 4	NP_689922.3
	STOX1	NM_001130161.4		c.134C>G	p.Ala45Gly	missense	Exon 1 of 5	NP_001123633.1	Q6ZVD7-1
	STOX1	NM_001130159.3		c.134C>G	p.Ala45Gly	missense	Exon 1 of 4	NP_001123631.1	Q6ZVD7-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STOX1	ENST00000298596.11	TSL:1 MANE Select	c.134C>G	p.Ala45Gly	missense	Exon 1 of 4	ENSP00000298596.6	Q6ZVD7-1
	STOX1	ENST00000399169.8	TSL:1	c.134C>G	p.Ala45Gly	missense	Exon 1 of 5	ENSP00000382121.4	Q6ZVD7-1
	STOX1	ENST00000399165.8	TSL:1	c.134C>G	p.Ala45Gly	missense	Exon 1 of 4	ENSP00000382118.4	Q6ZVD7-2

Frequencies

GnomAD3 genomes AF: 0.0000184 AC: 2 AN: 108404 Hom.: 0 Cov.: 13

Gnomad AFR AF: 0.0000702

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 8

GnomAD4 genome AF: 0.0000184 AC: 2 AN: 108474 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 52672

African (AFR) AF: 0.0000700 AC: 2 AN: 28570

American (AMR) AF: 0.00 AC: 0 AN: 11878

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2728

East Asian (EAS) AF: 0.00 AC: 0 AN: 3236

South Asian (SAS) AF: 0.00 AC: 0 AN: 3026

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 252

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50482

Other (OTH) AF: 0.00 AC: 0 AN: 1416

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000189

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.018	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.021	T
Eigen	Uncertain	0.23
Eigen_PC	Benign	0.21
FATHMM_MKL	Benign	0.45	N
LIST_S2	Benign	0.63	T
M_CAP	Pathogenic	0.99	D
MetaRNN	Benign	0.42	T
MetaSVM	Uncertain	-0.21	T
MutationAssessor	Benign	0.95	L
PhyloP100		0.80
PROVEAN	Benign	-1.2	N
REVEL	Uncertain	0.34
Sift	Benign	0.15	T
Sift4G	Benign	0.39	T
Polyphen		1.0	D
Vest4		0.24
MutPred		0.35		Gain of loop (P = 0.0045)
MVP		0.88
MPC		0.28
ClinPred		0.73	D
GERP RS		4.5
PromoterAI		-0.015	Neutral
Varity_R		0.12
gMVP		0.066
Mutation Taster		=94/6	polymorphism

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

Other links and lift over

dbSNP: rs1386133319; hg19: chr10-70587514;