rs1417939

Variant names:

• chr10-68874648-G-A
• rs1417939
• NM_152709.5:c.311-7310G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-68874648-G-A
• chr10-68874648-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152709.5(STOX1):​c.311-7310G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 132,710 control chromosomes in the GnomAD database, including 32,256 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 0.73 (32256 hom., cov: 24)
• Consequence: STOX1 NM_152709.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 2 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

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.311-7310G>A		intron	N/A	NP_689922.3
	STOX1	NM_001130161.4		c.311-7310G>A		intron	N/A	NP_001123633.1	Q6ZVD7-1
	STOX1	NM_001130159.3		c.311-7310G>A		intron	N/A	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.311-7310G>A		intron	N/A	ENSP00000298596.6	Q6ZVD7-1
	STOX1	ENST00000399169.8	TSL:1	c.311-7310G>A		intron	N/A	ENSP00000382121.4	Q6ZVD7-1
	STOX1	ENST00000399165.8	TSL:1	c.311-7310G>A		intron	N/A	ENSP00000382118.4	Q6ZVD7-2

Frequencies

GnomAD3 genomes AF: 0.729 AC: 96702 AN: 132658 Hom.: 32254 Cov.: 24

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.730

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.724

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.729 AC: 96724 AN: 132710 Hom.: 32256 Cov.: 24 AF XY: 0.731 AC XY: 47068 AN XY: 64400

African (AFR) AF: 0.678 AC: 23186 AN: 34178

American (AMR) AF: 0.698 AC: 9027 AN: 12930

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2255 AN: 3138

East Asian (EAS) AF: 0.911 AC: 4528 AN: 4970

South Asian (SAS) AF: 0.714 AC: 2930 AN: 4102

European-Finnish (FIN) AF: 0.768 AC: 6739 AN: 8774

Middle Eastern (MID) AF: 0.714 AC: 180 AN: 252

European-Non Finnish (NFE) AF: 0.744 AC: 45891 AN: 61658

Other (OTH) AF: 0.726 AC: 1348 AN: 1856

Alfa AF: 0.907 Hom.: 5077

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.50
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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: rs1417939; hg19: chr10-70634404;