X-145231305-A-G

Variant names:

• chrX-145231305-A-G
• rs5920468

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 0.54 (11747 hom., 17782 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• 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=-0.93).

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: 0.540 AC: 59693 AN: 110506 Hom.: 11751 Cov.: 23

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.522

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: 0.540 AC: 59737 AN: 110558 Hom.: 11747 Cov.: 23 AF XY: 0.542 AC XY: 17782 AN XY: 32824

African (AFR) AF: 0.603 AC: 18313 AN: 30388

American (AMR) AF: 0.667 AC: 6897 AN: 10345

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1037 AN: 2630

East Asian (EAS) AF: 0.846 AC: 2950 AN: 3485

South Asian (SAS) AF: 0.628 AC: 1630 AN: 2595

European-Finnish (FIN) AF: 0.535 AC: 3140 AN: 5866

Middle Eastern (MID) AF: 0.406 AC: 86 AN: 212

European-Non Finnish (NFE) AF: 0.466 AC: 24627 AN: 52862

Other (OTH) AF: 0.523 AC: 788 AN: 1506

Alfa AF: 0.483 Hom.: 23712

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.47
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs5920468; hg19: chrX-144312825;