X-87215978-A-G

Variant names:

• chrX-87215978-A-G
• rs5922395

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 0.87 (29365 hom., 27246 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• 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=-0.91).

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: 0.867 AC: 94171 AN: 108674 Hom.: 29374 Cov.: 22

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.960

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.876

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: 0.866 AC: 94182 AN: 108723 Hom.: 29365 Cov.: 22 AF XY: 0.871 AC XY: 27246 AN XY: 31271

African (AFR) AF: 0.700 AC: 20961 AN: 29956

American (AMR) AF: 0.928 AC: 9351 AN: 10073

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 2404 AN: 2609

East Asian (EAS) AF: 0.899 AC: 3084 AN: 3431

South Asian (SAS) AF: 0.947 AC: 2388 AN: 2521

European-Finnish (FIN) AF: 0.960 AC: 5410 AN: 5637

Middle Eastern (MID) AF: 0.949 AC: 203 AN: 214

European-Non Finnish (NFE) AF: 0.929 AC: 48419 AN: 52130

Other (OTH) AF: 0.872 AC: 1281 AN: 1469

Alfa AF: 0.896 Hom.: 94766

Bravo AF: 0.860

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.68
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs5922395; hg19: chrX-86470981;