chrX-127976473-A-G

Position:

• chrX-127976473-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 0.80 (24859 hom., 25906 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).

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: 0.796 AC: 87863 AN: 110420 Hom.: 24870 Cov.: 22 AF XY: 0.793 AC XY: 25874 AN XY: 32636

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.785

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.798

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: 0.795 AC: 87877 AN: 110468 Hom.: 24859 Cov.: 22 AF XY: 0.792 AC XY: 25906 AN XY: 32694

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.931

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.785

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.800

Alfa AF: 0.835 Hom.: 101064

Bravo AF: 0.783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2032468; hg19: chrX-127110452;