rs13106255

Variant names:

• chr4-183841547-G-A
• rs13106255
• ENST00000513034.3:c.364+43492G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STOX2	NR_132761.1	n.34+43492G>A		intron_variant	Intron 1 of 2
STOX2	XM_017008466.2	c.-21+43492G>A		intron_variant	Intron 1 of 2		XP_016863955.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STOX2	ENST00000513034.3	c.364+43492G>A		intron_variant	Intron 1 of 2	3		ENSP00000422118.3

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

African (AFR) AF: 0.746 AC: 30921 AN: 41438

American (AMR) AF: 0.865 AC: 13209 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3103 AN: 3472

East Asian (EAS) AF: 0.783 AC: 4053 AN: 5174

South Asian (SAS) AF: 0.882 AC: 4256 AN: 4824

European-Finnish (FIN) AF: 0.901 AC: 9522 AN: 10570

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.856 AC: 58208 AN: 68000

Other (OTH) AF: 0.858 AC: 1811 AN: 2110

Alfa AF: 0.847 Hom.: 242056

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs13106255; hg19: chr4-184762700;