X-15882205-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Homozygotes in GnomAd at 25913 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.811 AC: 89817 AN: 110804 Hom.: 25913 Cov.: 23 AF XY: 0.814 AC XY: 26855 AN XY: 32988

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

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.878

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.823

Alfa AF: 0.628 Hom.: 3434

Bravo AF: 0.833

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs798159; hg19: chrX-15900328;