rs5905613

chrX-43648052-T-C

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 0.62 (15855 hom., 19845 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd at 15855 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: 0.623 AC: 68496 AN: 109948 Hom.: 15855 Cov.: 22 AF XY: 0.615 AC XY: 19812 AN XY: 32218

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.657

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: 0.623 AC: 68526 AN: 110007 Hom.: 15855 Cov.: 22 AF XY: 0.615 AC XY: 19845 AN XY: 32287

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.656

Alfa AF: 0.697 Hom.: 63165

Bravo AF: 0.636

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5905613; hg19: chrX-43507300;