rs4301558

chrX-43652206-C-AchrX-43652206-C-GchrX-43652206-C-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 0.69 (19098 hom., 22132 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BS2: High Homozygotes in GnomAd at 19096 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: 0.690 AC: 76299 AN: 110579 Hom.: 19096 Cov.: 23 AF XY: 0.673 AC XY: 22087 AN XY: 32837

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.698

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.690

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: 0.690 AC: 76341 AN: 110632 Hom.: 19098 Cov.: 23 AF XY: 0.673 AC XY: 22132 AN XY: 32900

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.706

Gnomad4 OTH AF: 0.686

Alfa AF: 0.696 Hom.: 5543

Bravo AF: 0.702

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.50
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4301558; hg19: chrX-43511454;