rs1569893

Variant names:

• chrX-132006309-G-T
• rs1569893

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 0.76 (22824 hom., 24750 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

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: 0.762 AC: 84085 AN: 110397 Hom.: 22817 Cov.: 22

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.907

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.759

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: 0.762 AC: 84143 AN: 110448 Hom.: 22824 Cov.: 22 AF XY: 0.757 AC XY: 24750 AN XY: 32714

African (AFR) AF: 0.827 AC: 25150 AN: 30422

American (AMR) AF: 0.776 AC: 8102 AN: 10437

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 1760 AN: 2632

East Asian (EAS) AF: 0.542 AC: 1842 AN: 3400

South Asian (SAS) AF: 0.696 AC: 1787 AN: 2569

European-Finnish (FIN) AF: 0.720 AC: 4197 AN: 5831

Middle Eastern (MID) AF: 0.702 AC: 151 AN: 215

European-Non Finnish (NFE) AF: 0.747 AC: 39399 AN: 52762

Other (OTH) AF: 0.759 AC: 1141 AN: 1503

Alfa AF: 0.751 Hom.: 45604

Bravo AF: 0.772

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.31
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs1569893; hg19: chrX-131140337;