chrX-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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs792952; hg19: chrX-67983123;