rs1781115

Positions:

• chrX-124186482-T-C

Variant summary

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

The variant allele was found at a frequency of 0.439 in 111,751 control chromosomes in the GnomAD database, including 8,367 homozygotes. There are 14,758 hemizygotes in GnomAD. 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 0.44 (8367 hom., 14758 hem., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.124186482T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAG2	ENST00000469481.1	n.453+182735T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.439 AC: 49077 AN: 111696 Hom.: 8366 Cov.: 24 AF XY: 0.434 AC XY: 14726 AN XY: 33906

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.439 AC: 49108 AN: 111751 Hom.: 8367 Cov.: 24 AF XY: 0.434 AC XY: 14758 AN XY: 33969

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.438

Alfa AF: 0.369 Hom.: 32478

Bravo AF: 0.470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	7.2
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1781115; hg19: chrX-123320332;