rs13106255

Positions:

• chr4-183841547-G-A
• chr4-183841547-G-C

Variant summary

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

The ENST00000513034.3(STOX2):​c.364+43492G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,072 control chromosomes in the GnomAD database, including 52,621 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 0.83 (52621 hom., cov: 31)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.86 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STOX2	XM_017008466.2	c.-21+43492G>A		intron_variant
STOX2	NR_132761.1	n.34+43492G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STOX2	ENST00000513034.3	c.364+43492G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126038 AN: 151952 Hom.: 52568 Cov.: 31

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.856

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.830 AC: 126148 AN: 152072 Hom.: 52621 Cov.: 31 AF XY: 0.833 AC XY: 61905 AN XY: 74336

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.894

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.856

Gnomad4 OTH AF: 0.858

Alfa AF: 0.854 Hom.: 111614

Bravo AF: 0.822

Asia WGS AF: 0.835 AC: 2904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.011
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13106255; hg19: chr4-184762700;