X-51954098-C-T

Position:

• chrX-51954098-C-T

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 0.67 (17599 hom., 21914 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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: 0.669 AC: 73821 AN: 110287 Hom.: 17595 Cov.: 23 AF XY: 0.673 AC XY: 21897 AN XY: 32543

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.696

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: 0.669 AC: 73837 AN: 110336 Hom.: 17599 Cov.: 23 AF XY: 0.672 AC XY: 21914 AN XY: 32602

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.868

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.699

Alfa AF: 0.691 Hom.: 30167

Bravo AF: 0.681

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4131729; hg19: chrX-51697194;