X-66053345-T-G

Position:

• chrX-66053345-T-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 0.65 (12871 hom., 2525 hem., cov: 9)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.66053345T>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.653 AC: 35913 AN: 55024 Hom.: 12864 Cov.: 9 AF XY: 0.301 AC XY: 2519 AN XY: 8380

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.685

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: 0.652 AC: 35941 AN: 55103 Hom.: 12871 Cov.: 9 AF XY: 0.300 AC XY: 2525 AN XY: 8419

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.629

Gnomad4 ASJ AF: 0.835

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.687

Alfa AF: 0.749 Hom.: 4733

Bravo AF: 0.773

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	10
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599958; hg19: chrX-65273187;