X-90549128-A-G

Variant names:

• chrX-90549128-A-G
• rs2755459

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 0.71 (20011 hom., 20942 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).

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: 0.709 AC: 76187 AN: 107520 Hom.: 20025 Cov.: 20

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.924

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.726

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: 0.708 AC: 76193 AN: 107572 Hom.: 20011 Cov.: 20 AF XY: 0.694 AC XY: 20942 AN XY: 30186

African (AFR) AF: 0.557 AC: 16638 AN: 29851

American (AMR) AF: 0.801 AC: 7999 AN: 9988

Ashkenazi Jewish (ASJ) AF: 0.830 AC: 2144 AN: 2583

East Asian (EAS) AF: 0.740 AC: 2494 AN: 3369

South Asian (SAS) AF: 0.646 AC: 1574 AN: 2438

European-Finnish (FIN) AF: 0.737 AC: 3894 AN: 5282

Middle Eastern (MID) AF: 0.788 AC: 171 AN: 217

European-Non Finnish (NFE) AF: 0.766 AC: 39627 AN: 51737

Other (OTH) AF: 0.719 AC: 1035 AN: 1439

Alfa AF: 0.742 Hom.: 6051

Bravo AF: 0.713

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.28
PhyloP100		-2.3

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: rs2755459;

hg19: chrX-89804127;