X-90549128-A-G

Position:

• chrX-90549128-A-G

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 0.71 (20011 hom., 20942 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.90549128A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.709 AC: 76187 AN: 107520 Hom.: 20025 Cov.: 20 AF XY: 0.694 AC XY: 20907 AN XY: 30124

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.726

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: 0.708 AC: 76193 AN: 107572 Hom.: 20011 Cov.: 20 AF XY: 0.694 AC XY: 20942 AN XY: 30186

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.737

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.719

Alfa AF: 0.742 Hom.: 6051

Bravo AF: 0.713

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2755459; hg19: chrX-89804127;