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. Variant got -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

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 -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STOX1	NM_152709.5	c.311-7310G>A		intron_variant	Intron 1 of 3	ENST00000298596.11	NP_689922.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STOX1	ENST00000298596.11	c.311-7310G>A		intron_variant	Intron 1 of 3	1	NM_152709.5	ENSP00000298596.6

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

Gnomad4 AFR AF: 0.678

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.726

Alfa AF: 0.907 Hom.: 5077

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.50

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: rs1417939; hg19: chr10-70634404;