rs7682282

chr4-183836284-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513034.3(STOX2):c.364+38229G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 151,976 control chromosomes in the GnomAD database, including 25,250 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 0.57 (25250 hom., cov: 32)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

Genes affected

STOX2 (HGNC:25450): (storkhead box 2) This gene encodes a Storkhead-box_winged-helix domain containing protein. This protein is differentially expressed in decidual tissue and may be involved in the susceptibility to pre-eclampsia with fetal growth restriction. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

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 = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STOX2	XM_017008466.2	c.-21+38229G>A		intron_variant
STOX2	NR_132761.1	n.34+38229G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STOX2	ENST00000513034.3	c.364+38229G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86773 AN: 151858 Hom.: 25245 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.571 AC: 86816 AN: 151976 Hom.: 25250 Cov.: 32 AF XY: 0.577 AC XY: 42887 AN XY: 74282

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.844

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.587

Alfa AF: 0.583 Hom.: 31875

Bravo AF: 0.562

Asia WGS AF: 0.662 AC: 2301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.23
Dann	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7682282; hg19: chr4-184757437;