X-71203425-T-C

Variant names:

• chrX-71203425-T-C
• rs4844292

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 0.63 (16955 hom., 18284 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• 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=-1.02).

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: 0.627 AC: 66872 AN: 106585 Hom.: 16947 Cov.: 20

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.656

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: 0.628 AC: 66925 AN: 106623 Hom.: 16955 Cov.: 20 AF XY: 0.622 AC XY: 18284 AN XY: 29379

African (AFR) AF: 0.924 AC: 27226 AN: 29451

American (AMR) AF: 0.641 AC: 6267 AN: 9772

Ashkenazi Jewish (ASJ) AF: 0.683 AC: 1752 AN: 2567

East Asian (EAS) AF: 0.752 AC: 2491 AN: 3311

South Asian (SAS) AF: 0.606 AC: 1452 AN: 2398

European-Finnish (FIN) AF: 0.394 AC: 2077 AN: 5267

Middle Eastern (MID) AF: 0.698 AC: 139 AN: 199

European-Non Finnish (NFE) AF: 0.468 AC: 24123 AN: 51559

Other (OTH) AF: 0.663 AC: 960 AN: 1449

Alfa AF: 0.560 Hom.: 4322

Bravo AF: 0.657

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.1

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: rs4844292; hg19: chrX-70423275;