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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;