rs5918577

Variant names:

• chrX-66067738-A-C
• rs5918577

Your query was ambiguous. Multiple possible variants found:

• chrX-66067738-A-C
• chrX-66067738-A-G

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 0.66 (20518 hom., 15413 hem., cov: 17)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.335
• 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=-0.94).

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: 0.661 AC: 66129 AN: 100089 Hom.: 20527 Cov.: 17

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.817

Gnomad NFE AF: 0.862

Gnomad OTH AF: 0.723

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: 0.660 AC: 66112 AN: 100128 Hom.: 20518 Cov.: 17 AF XY: 0.646 AC XY: 15413 AN XY: 23858

African (AFR) AF: 0.177 AC: 4993 AN: 28251

American (AMR) AF: 0.768 AC: 7231 AN: 9414

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2025 AN: 2490

East Asian (EAS) AF: 0.999 AC: 2930 AN: 2934

South Asian (SAS) AF: 0.886 AC: 1655 AN: 1867

European-Finnish (FIN) AF: 0.841 AC: 3334 AN: 3964

Middle Eastern (MID) AF: 0.802 AC: 146 AN: 182

European-Non Finnish (NFE) AF: 0.862 AC: 42268 AN: 49043

Other (OTH) AF: 0.726 AC: 984 AN: 1356

Alfa AF: 0.695 Hom.: 22974

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.2
DANN	Benign	0.22
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs5918577; hg19: chrX-65287580;