chrX-87215978-A-G

Position:

• chrX-87215978-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 0.87 (29365 hom., 27246 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

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.87215978A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.867 AC: 94171 AN: 108674 Hom.: 29374 Cov.: 22 AF XY: 0.872 AC XY: 27217 AN XY: 31212

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.876

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: 0.866 AC: 94182 AN: 108723 Hom.: 29365 Cov.: 22 AF XY: 0.871 AC XY: 27246 AN XY: 31271

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.960

Gnomad4 NFE AF: 0.929

Gnomad4 OTH AF: 0.872

Alfa AF: 0.915 Hom.: 67315

Bravo AF: 0.860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5922395; hg19: chrX-86470981;