4-183874954-T-A

Position:

• chr4-183874954-T-A

Variant summary

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

The ENST00000513034.3(STOX2):​c.364+76899T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.051 (15 hom., cov: 0)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

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]

STOX2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STOX2	XM_017008466.2	c.-21+76899T>A		intron_variant			XP_016863955.2
STOX2	NR_132761.1	n.34+76899T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STOX2	ENST00000513034.3	c.364+76899T>A		intron_variant		3		ENSP00000422118.3
STOX2	ENST00000511250.1	n.413+21111T>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0509 AC: 1053 AN: 20698 Hom.: 15 Cov.: 0

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0450

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.00568

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0558

Gnomad OTH AF: 0.0561

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

GnomAD4 genome AF: 0.0509 AC: 1053 AN: 20694 Hom.: 15 Cov.: 0 AF XY: 0.0508 AC XY: 442 AN XY: 8700

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.00568

Gnomad4 NFE AF: 0.0558

Gnomad4 OTH AF: 0.0561

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10020901; hg19: chr4-184796107;