rs5923859

chrX-87172358-A-G

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 0.56 (12680 hom., 17587 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BS2: High Homozygotes in GnomAd at 12684 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: 0.556 AC: 61233 AN: 110115 Hom.: 12684 Cov.: 23 AF XY: 0.542 AC XY: 17570 AN XY: 32409

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.556

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: 0.556 AC: 61241 AN: 110163 Hom.: 12680 Cov.: 23 AF XY: 0.542 AC XY: 17587 AN XY: 32467

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.556

Alfa AF: 0.598 Hom.: 5131

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5923859; hg19: chrX-86427361;