rs5958390

Positions:

• chrX-124116647-G-A
• chrX-124116647-G-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.67 (18331 hom., 21663 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.124116647G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAG2	ENST00000469481.1	n.453+112900G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.673 AC: 73958 AN: 109901 Hom.: 18345 Cov.: 22 AF XY: 0.673 AC XY: 21633 AN XY: 32163

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.676

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.673 AC: 73964 AN: 109952 Hom.: 18331 Cov.: 22 AF XY: 0.672 AC XY: 21663 AN XY: 32224

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.729

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.673

Alfa AF: 0.726 Hom.: 8956

Bravo AF: 0.663

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5958390; hg19: chrX-123250497;