X-84669362-A-G

Position:

• chrX-84669362-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 0.74 (21868 hom., 24569 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.84669362A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.735 AC: 81276 AN: 110515 Hom.: 21879 Cov.: 23 AF XY: 0.748 AC XY: 24526 AN XY: 32771

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.784

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.787

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: 0.735 AC: 81300 AN: 110568 Hom.: 21868 Cov.: 23 AF XY: 0.748 AC XY: 24569 AN XY: 32834

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.866

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.984

Gnomad4 SAS AF: 0.871

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.785

Alfa AF: 0.801 Hom.: 60946

Bravo AF: 0.727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5922075; hg19: chrX-83924370;