X-84770950-A-G

Position:

• chrX-84770950-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 0.88 (30328 hom., 29293 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.312

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.884 AC: 97929 AN: 110740 Hom.: 30339 Cov.: 23 AF XY: 0.889 AC XY: 29240 AN XY: 32896

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.916

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.918

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: 0.884 AC: 97966 AN: 110795 Hom.: 30328 Cov.: 23 AF XY: 0.889 AC XY: 29293 AN XY: 32961

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.896

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.913

Alfa AF: 0.864 Hom.: 30003

Bravo AF: 0.889

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4828291; hg19: chrX-84025957;