X-28214936-G-A

Variant names:

• chrX-28214936-G-A
• rs5971305

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 0.77 (22925 hom., 25316 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.767 AC: 84813 AN: 110562 Hom.: 22919 Cov.: 23

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.676

Gnomad NFE AF: 0.719

Gnomad OTH AF: 0.759

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: 0.767 AC: 84879 AN: 110615 Hom.: 22925 Cov.: 23 AF XY: 0.771 AC XY: 25316 AN XY: 32837

African (AFR) AF: 0.829 AC: 25239 AN: 30444

American (AMR) AF: 0.803 AC: 8324 AN: 10369

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 1872 AN: 2638

East Asian (EAS) AF: 0.909 AC: 3179 AN: 3498

South Asian (SAS) AF: 0.753 AC: 1947 AN: 2584

European-Finnish (FIN) AF: 0.779 AC: 4572 AN: 5869

Middle Eastern (MID) AF: 0.664 AC: 144 AN: 217

European-Non Finnish (NFE) AF: 0.719 AC: 37965 AN: 52812

Other (OTH) AF: 0.762 AC: 1149 AN: 1507

Alfa AF: 0.741 Hom.: 93071

Bravo AF: 0.778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.059
DANN	Benign	0.47
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs5971305; hg19: chrX-28233053;