rs4473816

chrX-51667658-G-AchrX-51667658-G-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

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 0.74 (21638 hom., 24050 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.934

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BS2: High Homozygotes in GnomAd at 21636 gene

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: 0.743 AC: 81653 AN: 109864 Hom.: 21636 Cov.: 23 AF XY: 0.745 AC XY: 24009 AN XY: 32214

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.749

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: 0.743 AC: 81692 AN: 109899 Hom.: 21638 Cov.: 23 AF XY: 0.746 AC XY: 24050 AN XY: 32259

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.926

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.752

Alfa AF: 0.667 Hom.: 8997

Bravo AF: 0.764

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.19
Dann	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4473816; hg19: chrX-51410590;