chrX-124190570-G-A

Position:

• chrX-124190570-G-A

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 0.55 (12351 hom., 17905 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.812

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.124190570G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAG2	ENST00000469481.1	n.453+186823G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.550 AC: 60664 AN: 110358 Hom.: 12349 Cov.: 22 AF XY: 0.548 AC XY: 17867 AN XY: 32616

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.547

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: 0.550 AC: 60701 AN: 110409 Hom.: 12351 Cov.: 22 AF XY: 0.548 AC XY: 17905 AN XY: 32677

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.553

Alfa AF: 0.491 Hom.: 32461

Bravo AF: 0.574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1279795; hg19: chrX-123324420;