X-100875448-A-G

Variant names:

• chrX-100875448-A-G
• rs5921682

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 0.60 (14862 hom., 19252 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

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: 0.599 AC: 65813 AN: 109850 Hom.: 14861 Cov.: 22

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.573

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: 0.599 AC: 65838 AN: 109903 Hom.: 14862 Cov.: 22 AF XY: 0.598 AC XY: 19252 AN XY: 32199

African (AFR) AF: 0.830 AC: 25053 AN: 30185

American (AMR) AF: 0.568 AC: 5834 AN: 10277

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1286 AN: 2623

East Asian (EAS) AF: 0.436 AC: 1517 AN: 3476

South Asian (SAS) AF: 0.649 AC: 1674 AN: 2578

European-Finnish (FIN) AF: 0.611 AC: 3512 AN: 5744

Middle Eastern (MID) AF: 0.500 AC: 107 AN: 214

European-Non Finnish (NFE) AF: 0.489 AC: 25749 AN: 52630

Other (OTH) AF: 0.571 AC: 858 AN: 1503

Alfa AF: 0.553 Hom.: 22376

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.039
DANN	Benign	0.44
PhyloP100		-1.7

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: rs5921682; hg19: chrX-100130437;