X-18133269-A-G

Position:

• chrX-18133269-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 0.64 (16598 hom., 20390 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.18133269A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.643 AC: 70788 AN: 110025 Hom.: 16595 Cov.: 22 AF XY: 0.630 AC XY: 20341 AN XY: 32295

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.624

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: 0.644 AC: 70834 AN: 110076 Hom.: 16598 Cov.: 22 AF XY: 0.630 AC XY: 20390 AN XY: 32356

Gnomad4 AFR AF: 0.657

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.626

Alfa AF: 0.663 Hom.: 72816

Bravo AF: 0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs763056; hg19: chrX-18151389;