rs5928917

Positions:

• chrX-35564261-C-A

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 0.63 (15976 hom., 20245 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).

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: 0.635 AC: 69721 AN: 109857 Hom.: 15985 Cov.: 22 AF XY: 0.630 AC XY: 20224 AN XY: 32125

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.651

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: 0.634 AC: 69724 AN: 109911 Hom.: 15976 Cov.: 22 AF XY: 0.629 AC XY: 20245 AN XY: 32189

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.682

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.646

Alfa AF: 0.645 Hom.: 46945

Bravo AF: 0.645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5928917; hg19: chrX-35582378;