rs5928917

Variant names:

• chrX-35564261-C-A
• rs5928917

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 0.63 (15976 hom., 20245 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.635 AC: 69721 AN: 109857 Hom.: 15985 Cov.: 22

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.651

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: 0.634 AC: 69724 AN: 109911 Hom.: 15976 Cov.: 22 AF XY: 0.629 AC XY: 20245 AN XY: 32189

African (AFR) AF: 0.586 AC: 17734 AN: 30266

American (AMR) AF: 0.682 AC: 7007 AN: 10281

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 1805 AN: 2627

East Asian (EAS) AF: 0.840 AC: 2878 AN: 3428

South Asian (SAS) AF: 0.431 AC: 1122 AN: 2602

European-Finnish (FIN) AF: 0.627 AC: 3590 AN: 5729

Middle Eastern (MID) AF: 0.707 AC: 145 AN: 205

European-Non Finnish (NFE) AF: 0.648 AC: 34084 AN: 52607

Other (OTH) AF: 0.646 AC: 970 AN: 1502

Alfa AF: 0.645 Hom.: 67645

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.20
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs5928917; hg19: chrX-35582378;