X-68763280-C-G

Variant names:

• chrX-68763280-C-G
• rs792952

Variant summary

Our verdict is Likely benign. The variant received -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 0.83 (26846 hom., 27100 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.831 AC: 91585 AN: 110251 Hom.: 26849 Cov.: 23

Gnomad AFR AF: 0.874

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.882

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.831

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: 0.831 AC: 91619 AN: 110301 Hom.: 26846 Cov.: 23 AF XY: 0.833 AC XY: 27100 AN XY: 32533

African (AFR) AF: 0.874 AC: 26506 AN: 30336

American (AMR) AF: 0.885 AC: 9128 AN: 10312

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2205 AN: 2633

East Asian (EAS) AF: 0.837 AC: 2901 AN: 3467

South Asian (SAS) AF: 0.865 AC: 2195 AN: 2539

European-Finnish (FIN) AF: 0.815 AC: 4738 AN: 5813

Middle Eastern (MID) AF: 0.865 AC: 186 AN: 215

European-Non Finnish (NFE) AF: 0.795 AC: 41967 AN: 52808

Other (OTH) AF: 0.832 AC: 1251 AN: 1503

Alfa AF: 0.670 Hom.: 2703

Bravo AF: 0.843

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		0.022

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs792952; hg19: chrX-67983123;