rs13136503

Variant names:

• chr4-183815882-G-A
• rs13136503
• ENST00000513034.3:c.364+17827G>A

Variant summary

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

The ENST00000513034.3(STOX2):​c.364+17827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,198 control chromosomes in the GnomAD database, including 6,243 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 0.28 (6243 hom., cov: 33)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STOX2	NR_132761.1	n.34+17827G>A		intron_variant	Intron 1 of 2
STOX2	XM_017008466.2	c.-21+17827G>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+17827G>A		intron_variant	Intron 1 of 2	3		ENSP00000422118.3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42158 AN: 152080 Hom.: 6223 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.277 AC: 42232 AN: 152198 Hom.: 6243 Cov.: 33 AF XY: 0.274 AC XY: 20427 AN XY: 74428

African (AFR) AF: 0.381 AC: 15825 AN: 41502

American (AMR) AF: 0.277 AC: 4243 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1013 AN: 3472

East Asian (EAS) AF: 0.171 AC: 888 AN: 5194

South Asian (SAS) AF: 0.315 AC: 1519 AN: 4828

European-Finnish (FIN) AF: 0.157 AC: 1666 AN: 10606

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16105 AN: 67988

Other (OTH) AF: 0.273 AC: 575 AN: 2110

Alfa AF: 0.281 Hom.: 3993

Bravo AF: 0.292

Asia WGS AF: 0.285 AC: 990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.084
DANN	Benign	0.32
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13136503; hg19: chr4-184737035;