X-4266308-A-G

Position:

• chrX-4266308-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 0.59 (15783 hom., 17926 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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: 0.594 AC: 65007 AN: 109380 Hom.: 15779 Cov.: 21 AF XY: 0.564 AC XY: 17870 AN XY: 31688

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.568

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.567

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: 0.594 AC: 65048 AN: 109435 Hom.: 15783 Cov.: 21 AF XY: 0.565 AC XY: 17926 AN XY: 31753

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.560

Alfa AF: 0.526 Hom.: 12633

Bravo AF: 0.607

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.32
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6529954; hg19: chrX-4184349;