X-114556657-T-C

Variant names:

• chrX-114556657-T-C
• rs519161

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 0.81 (25774 hom., 26721 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• 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=-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: 0.815 AC: 89889 AN: 110298 Hom.: 25784 Cov.: 23

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.864

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.834

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: 0.815 AC: 89907 AN: 110348 Hom.: 25774 Cov.: 23 AF XY: 0.820 AC XY: 26721 AN XY: 32590

African (AFR) AF: 0.778 AC: 23615 AN: 30367

American (AMR) AF: 0.807 AC: 8288 AN: 10270

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2047 AN: 2628

East Asian (EAS) AF: 0.975 AC: 3425 AN: 3513

South Asian (SAS) AF: 0.891 AC: 2325 AN: 2609

European-Finnish (FIN) AF: 0.864 AC: 5012 AN: 5799

Middle Eastern (MID) AF: 0.742 AC: 155 AN: 209

European-Non Finnish (NFE) AF: 0.819 AC: 43235 AN: 52779

Other (OTH) AF: 0.836 AC: 1252 AN: 1498

Alfa AF: 0.752 Hom.: 7609

Bravo AF: 0.806

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.16

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: rs519161; hg19: chrX-113791114;