rs28382699

Variant names:

• chrX-123858916-C-T
• rs28382699

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;