4-183804753-C-T

Position:

• chr4-183804753-C-T

Variant summary

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

The ENST00000513034.3(STOX2):​c.364+6698C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,160 control chromosomes in the GnomAD database, including 42,348 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 0.72 (42348 hom., cov: 33)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STOX2	XM_017008466.2	c.-21+6698C>T		intron_variant			XP_016863955.2
STOX2	NR_132761.1	n.34+6698C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STOX2	ENST00000513034.3	c.364+6698C>T		intron_variant		3		ENSP00000422118.3

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110252 AN: 152042 Hom.: 42348 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.897

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.831

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.725 AC: 110281 AN: 152160 Hom.: 42348 Cov.: 33 AF XY: 0.731 AC XY: 54398 AN XY: 74392

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.911

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.821

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.774

Alfa AF: 0.825 Hom.: 68571

Bravo AF: 0.707

Asia WGS AF: 0.852 AC: 2961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs930306; hg19: chr4-184725906;