X-71205125-G-A

Variant names:

• chrX-71205125-G-A
• rs9698457

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 (15079 hom., 19780 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

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: 66260 AN: 110656 Hom.: 15069 Cov.: 23

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.624

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: 66320 AN: 110706 Hom.: 15079 Cov.: 23 AF XY: 0.600 AC XY: 19780 AN XY: 32956

African (AFR) AF: 0.827 AC: 25235 AN: 30522

American (AMR) AF: 0.631 AC: 6522 AN: 10337

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 1794 AN: 2645

East Asian (EAS) AF: 0.750 AC: 2619 AN: 3490

South Asian (SAS) AF: 0.607 AC: 1603 AN: 2643

European-Finnish (FIN) AF: 0.403 AC: 2360 AN: 5850

Middle Eastern (MID) AF: 0.700 AC: 147 AN: 210

European-Non Finnish (NFE) AF: 0.466 AC: 24635 AN: 52820

Other (OTH) AF: 0.630 AC: 953 AN: 1513

Alfa AF: 0.526 Hom.: 3749

Bravo AF: 0.624

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.79

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: rs9698457; hg19: chrX-70424975;