X-15882205-A-G

Variant names:

• chrX-15882205-A-G
• rs798159

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 0.81 (25918 hom., 26915 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• 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=-0.89).

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: 0.811 AC: 89817 AN: 110804 Hom.: 25913 Cov.: 23

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.878

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.746

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.820

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: 0.811 AC: 89880 AN: 110857 Hom.: 25918 Cov.: 23 AF XY: 0.814 AC XY: 26915 AN XY: 33051

African (AFR) AF: 0.948 AC: 28906 AN: 30494

American (AMR) AF: 0.878 AC: 9166 AN: 10436

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 1930 AN: 2640

East Asian (EAS) AF: 0.988 AC: 3489 AN: 3532

South Asian (SAS) AF: 0.841 AC: 2194 AN: 2610

European-Finnish (FIN) AF: 0.756 AC: 4440 AN: 5870

Middle Eastern (MID) AF: 0.749 AC: 161 AN: 215

European-Non Finnish (NFE) AF: 0.715 AC: 37817 AN: 52882

Other (OTH) AF: 0.823 AC: 1243 AN: 1510

Alfa AF: 0.628 Hom.: 3434

Bravo AF: 0.833

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-0.22

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs798159; hg19: chrX-15900328;