X-71206265-A-T

Position:

• chrX-71206265-A-T

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 (15367 hom., 18205 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.603 AC: 64954 AN: 107650 Hom.: 15358 Cov.: 20 AF XY: 0.599 AC XY: 18149 AN XY: 30316

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.633

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: 0.604 AC: 65017 AN: 107700 Hom.: 15367 Cov.: 20 AF XY: 0.599 AC XY: 18205 AN XY: 30380

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.639

Alfa AF: 0.523 Hom.: 3138

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.1
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9698122; hg19: chrX-70426115;