X-71205125-G-A

Position:

• chrX-71205125-G-A

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 0.60 (15079 hom., 19780 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.71205125G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.599 AC: 66260 AN: 110656 Hom.: 15069 Cov.: 23 AF XY: 0.600 AC XY: 19729 AN XY: 32894

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.466

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: 0.599 AC: 66320 AN: 110706 Hom.: 15079 Cov.: 23 AF XY: 0.600 AC XY: 19780 AN XY: 32956

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.466

Gnomad4 OTH AF: 0.630

Alfa AF: 0.526 Hom.: 3749

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.73
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9698457; hg19: chrX-70424975;