chr4-183846368-T-C

Variant names:

• chr4-183846368-T-C
• rs7695711
• ENST00000513034.3:c.364+48313T>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+48313T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,946 control chromosomes in the GnomAD database, including 26,037 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 0.57 (26037 hom., cov: 31)
• Consequence: STOX2 ENST00000513034.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STOX2	NR_132761.1	n.34+48313T>C		intron_variant	Intron 1 of 2
STOX2	XM_017008466.2	c.-21+48313T>C		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+48313T>C		intron_variant	Intron 1 of 2	3		ENSP00000422118.3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86422 AN: 151828 Hom.: 26026 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.569 AC: 86459 AN: 151946 Hom.: 26037 Cov.: 31 AF XY: 0.575 AC XY: 42685 AN XY: 74234

African (AFR) AF: 0.366 AC: 15169 AN: 41450

American (AMR) AF: 0.587 AC: 8956 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2137 AN: 3468

East Asian (EAS) AF: 0.920 AC: 4754 AN: 5168

South Asian (SAS) AF: 0.600 AC: 2881 AN: 4804

European-Finnish (FIN) AF: 0.698 AC: 7340 AN: 10518

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43248 AN: 67954

Other (OTH) AF: 0.612 AC: 1294 AN: 2114

Alfa AF: 0.618 Hom.: 48820

Bravo AF: 0.559

Asia WGS AF: 0.728 AC: 2531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.0
DANN	Benign	0.68
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7695711; hg19: chr4-184767521;