X-118251602-A-G

Position:

• chrX-118251602-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 0.55 (12582 hom., 17843 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118251602A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.550 AC: 60907 AN: 110723 Hom.: 12590 Cov.: 23 AF XY: 0.541 AC XY: 17821 AN XY: 32939

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.551

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: 0.550 AC: 60911 AN: 110779 Hom.: 12582 Cov.: 23 AF XY: 0.541 AC XY: 17843 AN XY: 33005

Gnomad4 AFR AF: 0.448

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.549

Alfa AF: 0.602 Hom.: 6144

Bravo AF: 0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	13
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1218117; hg19: chrX-117385565;