X-12892203-G-A

Position:

• chrX-12892203-G-A

Variant summary

Our verdict is Likely benign. Variant got -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 (25371 hom., 23673 hem., cov: 20)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.806 AC: 86210 AN: 106898 Hom.: 25365 Cov.: 20 AF XY: 0.806 AC XY: 23625 AN XY: 29294

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.852

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.796

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: 0.807 AC: 86259 AN: 106940 Hom.: 25371 Cov.: 20 AF XY: 0.807 AC XY: 23673 AN XY: 29346

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.852

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.913

Gnomad4 FIN AF: 0.805

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.799

Alfa AF: 0.792 Hom.: 37371

Bravo AF: 0.814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.042
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179007; hg19: chrX-12910322;