X-18133269-A-G

Variant names:

• chrX-18133269-A-G
• rs763056

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 0.64 (16598 hom., 20390 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484
• 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=-0.84).

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: 0.643 AC: 70788 AN: 110025 Hom.: 16595 Cov.: 22

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.754

Gnomad NFE AF: 0.679

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: 0.644 AC: 70834 AN: 110076 Hom.: 16598 Cov.: 22 AF XY: 0.630 AC XY: 20390 AN XY: 32356

African (AFR) AF: 0.657 AC: 19848 AN: 30218

American (AMR) AF: 0.467 AC: 4855 AN: 10396

Ashkenazi Jewish (ASJ) AF: 0.742 AC: 1950 AN: 2628

East Asian (EAS) AF: 0.415 AC: 1440 AN: 3466

South Asian (SAS) AF: 0.558 AC: 1415 AN: 2534

European-Finnish (FIN) AF: 0.709 AC: 4098 AN: 5777

Middle Eastern (MID) AF: 0.767 AC: 165 AN: 215

European-Non Finnish (NFE) AF: 0.679 AC: 35757 AN: 52693

Other (OTH) AF: 0.626 AC: 932 AN: 1489

Alfa AF: 0.659 Hom.: 96474

Bravo AF: 0.629

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.48

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: rs763056;

hg19: chrX-18151389;