rs28382699

Positions:

• chrX-123858916-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.047 (157 hom., 1486 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

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: 0.0471 AC: 4871 AN: 103351 Hom.: 156 Cov.: 20 AF XY: 0.0525 AC XY: 1482 AN XY: 28235

Gnomad AFR AF: 0.00745

Gnomad AMI AF: 0.0119

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.0593

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.0850

Gnomad MID AF: 0.0874

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0459

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0471 AC: 4872 AN: 103387 Hom.: 157 Cov.: 20 AF XY: 0.0525 AC XY: 1486 AN XY: 28281

Gnomad4 AFR AF: 0.00747

Gnomad4 AMR AF: 0.0588

Gnomad4 ASJ AF: 0.0593

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.0850

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0546

Alfa AF: 0.0382 Hom.: 223

Bravo AF: 0.0445

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs28382699; hg19: chrX-122992766;