X-12892402-A-G

Position:

• chrX-12892402-A-G

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 0.82 (26120 hom., 26767 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390

Genes affected

(HGNC:):

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
		n.12892402A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.820 AC: 90325 AN: 110087 Hom.: 26116 Cov.: 22 AF XY: 0.827 AC XY: 26705 AN XY: 32301

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.862

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.860

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.808

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: 0.821 AC: 90386 AN: 110144 Hom.: 26120 Cov.: 22 AF XY: 0.827 AC XY: 26767 AN XY: 32368

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.860

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.810

Alfa AF: 0.796 Hom.: 58245

Bravo AF: 0.823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs179006; hg19: chrX-12910521;