X-89505727-C-G

Position:

• chrX-89505727-C-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 0.63 (17624 hom., 16477 hem., cov: 18)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.89505727C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.633 AC: 65577 AN: 103533 Hom.: 17629 Cov.: 18 AF XY: 0.625 AC XY: 16472 AN XY: 26341

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.868

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.743

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.668

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: 0.633 AC: 65565 AN: 103581 Hom.: 17624 Cov.: 18 AF XY: 0.624 AC XY: 16477 AN XY: 26399

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.669

Alfa AF: 0.480 Hom.: 1589

Bravo AF: 0.620

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs223692; hg19: chrX-88760726;