chrX-114576614-A-T

Variant names:

• chrX-114576614-A-T
• rs547536

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate

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 0.66 (16917 hom., 21127 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 6 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).

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: 0.657 AC: 72221 AN: 109861 Hom.: 16924 Cov.: 23

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.683

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: 0.657 AC: 72223 AN: 109910 Hom.: 16917 Cov.: 23 AF XY: 0.653 AC XY: 21127 AN XY: 32362

African (AFR) AF: 0.627 AC: 19067 AN: 30416

American (AMR) AF: 0.646 AC: 6639 AN: 10271

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 1651 AN: 2621

East Asian (EAS) AF: 0.832 AC: 2896 AN: 3482

South Asian (SAS) AF: 0.609 AC: 1599 AN: 2626

European-Finnish (FIN) AF: 0.720 AC: 4139 AN: 5750

Middle Eastern (MID) AF: 0.623 AC: 132 AN: 212

European-Non Finnish (NFE) AF: 0.660 AC: 34545 AN: 52360

Other (OTH) AF: 0.685 AC: 1031 AN: 1506

Alfa AF: 0.663 Hom.: 5190

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	11
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs547536; hg19: chrX-113811080;