rs547536

Positions:

• chrX-114576614-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

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 0.66 (16917 hom., 21127 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.25).

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: 0.657 AC: 72221 AN: 109861 Hom.: 16924 Cov.: 23 AF XY: 0.654 AC XY: 21112 AN XY: 32303

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.638

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.683

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: 0.657 AC: 72223 AN: 109910 Hom.: 16917 Cov.: 23 AF XY: 0.653 AC XY: 21127 AN XY: 32362

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.685

Alfa AF: 0.663 Hom.: 5190

Bravo AF: 0.653

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.25
CADD	Benign	11

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs547536; hg19: chrX-113811080;