chrX-117075605-C-T

Variant names:

• chrX-117075605-C-T
• rs5909759

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 0.88 (30578 hom., 28929 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• 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=-1.03).

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: 0.877 AC: 97049 AN: 110656 Hom.: 30583 Cov.: 23

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.910

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.877

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: 0.877 AC: 97078 AN: 110713 Hom.: 30578 Cov.: 23 AF XY: 0.879 AC XY: 28929 AN XY: 32917

African (AFR) AF: 0.681 AC: 20721 AN: 30409

American (AMR) AF: 0.852 AC: 8857 AN: 10390

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 2597 AN: 2649

East Asian (EAS) AF: 0.765 AC: 2665 AN: 3482

South Asian (SAS) AF: 0.872 AC: 2270 AN: 2603

European-Finnish (FIN) AF: 0.992 AC: 5815 AN: 5860

Middle Eastern (MID) AF: 0.912 AC: 196 AN: 215

European-Non Finnish (NFE) AF: 0.982 AC: 51946 AN: 52909

Other (OTH) AF: 0.878 AC: 1330 AN: 1514

Alfa AF: 0.910 Hom.: 21838

Bravo AF: 0.853

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5909759; hg19: chrX-116209573;